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1	\|\|\|\|\|\|\|\|\|\|\| ReadSeq supported formats (revised 30Dec92)
2	--------------------------------------------------------
3
4	-f[ormat=]Name Format name for output:
5	1. IG/Stanford 10. Olsen (in-only)
6	2. GenBank/GB 11. Phylip3.2
7	3. NBRF 12. Phylip
8	4. EMBL 13. Plain/Raw
9	5. GCG 14. PIR/CODATA
10	6. DNAStrider 15. MSF
11	7. Fitch 16. ASN.1
12	8. Pearson/Fasta 17. PAUP
13	9. Zuker (in-only) 18. Pretty (out-only)
14
15	In general, output supports only minimal subsets of each format
16	needed for sequence data exchanges. Features, descriptions
17	and other format-unique information is discarded.
18
19	Users of Olsen multi sequence editor (VMS). The Olsen format
20	here is produced with the print command:
21	print/out=some.file
22	Use Genbank output from readseq to produce a format that this
23	editor can read, and use the command
24	load/genbank some.file
25	Dan Davison has a VMS program that will convert to/from the
26	Olsen native binary data format. E-mail davison@uh.edu
27
28	Warning: Phylip format input is now supported (30Dec92), however the
29	auto-detection of Phylip format is very probabilistic and messy,
30	especially distinguishing sequential from interleaved versions. It
31	is not recommended that one use readseq to convert files from Phylip
32	format to others unless essential.
33
34
35
36	\|\|\|\|\|\|\|\|\|\|\| ReadSeq usage (revised 11Nov91)
37	--------------------------------------------------------
38
39	A. determine file format:
40
41	short skiplines; /* result: number of header lines to skip (or 0) */
42	short error; /* error result or 0 */
43	short format; /* resulting format code, see ureadseq.h */
44	char *filename = "Mysequence.file"
45
46	format = seqFileFormat( filename, &skiplines, &error);
47	if (error!=0) fail;
48
49	B. read number and list of sequences (optional)
50	short numseqs; /* resulting number of sequences found in file */
51	char seqlist; / list of sequence names, newline separated, 0 terminated */
52
53	seqlist = listSeqs( filename, skiplines, format, &numseqs, &error);
54	if (error!=0) display (seqlist);
55	free( seqlist);
56
57	C. read individual sequences as desired
58	short seqIndex; /* sequence index #, or == kListSeqs for listSeqs equivalent */
59	long seqlen; /* length of seq */
60	char seqid[256]; /* sequence name */
61	char seq; / sequence, 0 terminated, free when done */
62
63	seq = readSeq( seqIndex, filename, skiplines, format,
64	&seqlen, &numseqs, &error, seqid);
65	if (error!=0) manipulate(seq);
66	free(seq);
67
68	D. write sequences as desired
69	int nlines; /* number of lines of sequence written */
70	FILE* fout; /* open file pointer (stdout or other) */
71	short outform; /* output format, see ureadseq.h */
72
73	nlines = writeSeq( fout, seq, seqlen, format, outform, seqid);
74
75
76	Note (30Dec92): There is various processing done by the main program (in readseq.c),
77	rather than just in the subroutines (in ureadseq.c). Especially for interleaved
78	output formats, the writeSeq subroutine does not handle interleaving, nor some of
79	the formatting at the top and end of output files. While seqFileFormat, listSeqs,
80	and readSeq subroutines are fairly self-contained, the writeSeq depends a lot on
81	auxilliary processing. At some point, this may be revised so writeSeq is self-
82	contained.
83
84	Note 2: The NCBI toolkit (ftp from ncbi.nlm.nih.gov) is needed for the ASN.1 format
85	reading (see ureadasn.c). A bastard (but workable I hope) ASN.1 format is written
86	by writeSeq alone.
87
88
89
90	\|\|\|\|\|\|\|\|\|\|\| sequence formats....
91	---------------------------------------------------
92
93	stanford/IG
94	;comments
95	;...
96	seq1 info
97	abcd...
98	efgh1 (or 2 = terminator)
99	;another seq
100	;....
101	seq2 info
102	abcd...1
103	--- for e.g. ----
104	; Dro5s-T.Seq Length: 120 April 6, 1989 21:22 Check: 9487 ..
105	dro5stseq
106	GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGCGGGCG
107	GUUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCU1
108
109	; TOIG of: Dro5srna.Seq check: 9487 from: 1 to: 120
110	---------------------------------------------------
111
112	Genbank:
113	LOCUS seq1 ID..
114	...
115	ORIGIN ...
116	123456789abcdefg....(1st 9 columns are formatting)
117	hijkl...
118	// (end of sequence)
119	LOCUS seq2 ID ..
120	...
121	ORIGIN
122	abcd...
123	//
124	---------------------------------------------------
125
126	NBRF format: (from uwgcg ToNBRF)
127	>DL;DRO5SRNA
128	Iubio$Dua0:[Gilbertd.Gcg]Dro5srna.Seq;2 => DRO5SRNA
129
130	51 AAUUAAGCAG CGUCGCGGGC GGUUAGUACU UAGAUGGGGG ACCGCUUGGG
131	101 AACACCGCGU GUUGUUGGCC U
132
133	---------------------------------------------------
134
135	EMBL format
136	ID345 seq1 id (the 345 are spaces)
137	... other info
138	SQ345Sequence (the 3,4,5 are spaces)
139	abcd...
140	hijk...
141	// (! this is proper end string: 12Oct90)
142	ID seq2 id
143	...
144	SQ Sequence
145	abcd...
146	...
147	//
148	---------------------------------------------------
149
150	UW GCG Format:
151	comments of any form, up to ".." signal
152	signal line has seq id, and " Check: #### .."
153	only 1 seq/file
154
155	-- e.g. --- (GCG from GenBank)
156	LOCUS DROEST6 1819 bp ss-mRNA INV 31-AUG-1987
157	... much more ...
158	ORIGIN 1 bp upstream of EcoRI site; chromosome BK9 region 69A1.
159
160	INVERTEBRATE:DROEST6 Length: 1819 January 9, 1989 16:48 Check: 8008 ..
161
162	1 GAATTCGCCG GAGTGAGGAG CAACATGAAC TACGTGGGAC TGGGACTTAT
163
164	51 CATTGTGCTG AGCTGCCTTT GGCTCGGTTC GAACGCGAGT GATACAGATG
165
166
167	---------------------------------------------------
168
169	DNAStrider (Mac) = modified Stanford:
170	; ### from DNA Strider Friday, April 7, 1989 11:04:24 PM
171	; DNA sequence pBR322 4363 b.p. complete sequence
172	;
173	abcd...
174	efgh
175	// (end of sequence)
176	---------------------------------------------------
177
178	Fitch format:
179	Dro5srna.Seq
180	GCC AAC GAC CAU ACC ACG CUG AAU ACA UCG GUU CUC GUC CGA UCA CCG AAA UUA AGC AGC
181	GUC GCG GGC GGU UAG UAC UUA GAU GGG GGA CCG CUU GGG AAC ACC GCG UGU UGU UGG CCU
182	Droest6.Seq
183	GAA TTC GCC GGA GTG AGG AGC AAC ATG AAC TAC GTG GGA CTG GGA CTT ATC ATT GTG CTG
184	AGC TGC CTT TGG CTC GGT TCG AAC GCG AGT GAT ACA GAT GAC CCT CTG TTG GTG CAG CTG
185	---------------------------------------------------
186
187	W.Pearson/Fasta format:
188	>BOVPRL GenBank entry BOVPRL from omam file. 907 nucleotides.
189	TGCTTGGCTGAGGAGCCATAGGACGAGAGCTTCCTGGTGAAGTGTGTTTCTTGAAATCAT
190
191	---------------------------------------------------
192	Phylip version 3.2 format (e.g., DNAML):
193
194	5 13 YF (# seqs, #bases, YF)
195	Alpha AACGTGGCCAAAT
196	aaaagggccc... (continued sp. alpha)
197	Beta AAGGTCGCCAAAC
198	aaaagggccc... (continued sp. beta)
199	Gamma CATTTCGTCACAA
200	aaaagggccc... (continued sp. Gamma)
201	1234567890^-- bases must start in col 11, and run 'til #bases
202	(spaces & newlines are okay)
203	---------------------------------------------------
204	Phylip version 3.3 format (e.g., DNAML):
205
206	5 42 YF (# seqs, #bases, YF)
207	Turkey AAGCTNGGGC ATTTCAGGGT
208	Salmo gairAAGCCTTGGC AGTGCAGGGT
209	H. SapiensACCGGTTGGC CGTTCAGGGT
210	Chimp AAACCCTTGC CGTTACGCTT
211	Gorilla AAACCCTTGC CGGTACGCTT
212	1234567890^-- bases must start in col 11
213	!! this version interleaves the species -- contrary to
214	all other output formats.
215
216	GAGCCCGGGC AATACAGGGT AT
217	GAGCCGTGGC CGGGCACGGT AT
218	ACAGGTTGGC CGTTCAGGGT AA
219	AAACCGAGGC CGGGACACTC AT
220	AAACCATTGC CGGTACGCTT AA
221
222	---------------------------------------------------
223	Phylip version 3.4 format (e.g., DNAML)
224	-- Both Interleaved and sequential are permitted
225
226	5 13 (# seqs, #bases)
227	Alpha AACGTGGCCAAAT
228	aaaagggccc... (continued sp. alpha)
229	Beta AAGGTCGCCAAAC
230	aaaagggccc... (continued sp. beta)
231	Gamma CATTTCGTCACAA
232	aaaagggccc... (continued sp. Gamma)
233	1234567890^-- bases must start in col 11, and run 'til #bases
234	(spaces, newlines and numbers are are ignored)
235
236	---------------------------------------------------
237	Gary Olsen (multiple) sequence editor /print format:
238
239	!---------------------
240	!17Oct91 -- error in original copy of olsen /print format, shifted right 1 space
241	! here is correct copy:
242	301 40 Tb.thiop CGCAGCGAAA----------GCUNUGCUAAUACCGCAUA-CGnCCUG----------------------------------------------------- Tb.thiop
243	123456789012345678901
244	301 42 Rhc.purp CGUAGCGAAA----------GUUACGCUAAUACCGCAUA-UUCUGUG----------------------------------------------------- Rhc.purp
245
246	301 44 Rhc.gela nnngnCGAAA----------GCCGGAUUAAUACCGCAUA-CGACCUA----------------------------------------------------- Rhc.gela
247	!---------------------
248
249	RNase P RNA components. on 20-FEB-90 17:23:58
250
251	1 (E.c. pr ): Base pairing in Escherichia coli RNase P RNA.
252	2 (chrom ): Chromatium
253	:
254	12 (B.brevis): Bacillus brevis RNase P RNA, B. James.
255	13 ( 90% con): 90% conserved
256	14 (100% con): 100% conserved
257	15 (gram+ pr): pairing
258
259	1
260	RNase P RNA components. on 20-FEB-90 17:23:58
261
262	Posi- Sequence
263	tion: identity: Data:
264
265	1 1 E.c. pr <<<<<<<<<< {{{{{{{{<<:<<<<<<<<<<^<<<<<<====>>>> E.c. pr
266	1 2 chrom GGAGUCGGCCAGACAGUCGCUUCCGUCCU------------------ chrom
267	:
268	1 12 B.brevis AUGCAGGAAAUGCGGGUAGCCGCUGCCGCAAUCGUCU------------- B.brevis
269	1234567890123456789012 <! this should be 21 not 22,
270	! this example must be inset on left by 1 space from olsen /print files !
271	1 13 90% con G C G A CGC GC - - 90% con
272	1 14 100% con G A CGC 100% con
273	1 15 gram+ pr <<<<<<<<<< {{{{{{{{<<<<<<<<<<<<<=============== gram+ pr
274
275	60 1 E.c. pr >>>>>>^>>^>>>>:>> <<<^<<<< {{{{{ E.c. pr
276	60 2 chrom -----GGUG-ACGGGGGAGGAAAGUCCGG-GCUCCAU------------- chrom
277	: :
278	60 10 B.stearo ----UU-CG-GCCGUAGAGGAAAGUCCAUGCUCGCACGGUGCUGAGAUGC B.stearo
279
280
281	---------------------------------------------------
282	GCG MSF format
283	Title line
284
285	picorna.msf MSF: 100 Type: P January 17, 1991 17:53 Check: 541
286	..
287	Name: Cb3 Len: 100 Check: 7009 Weight: 1.00
288	Name: E Len: 100 Check: 60 Weight: 1.00
289
290	//
291
292	1 50
293	Cb3 ...gpvedai .......t.. aaigr..vad tvgtgptnse aipaltaaet
294	E gvenae.kgv tentna.tad fvaqpvylpe .nqt...... kv.affynrs
295
296	51 100
297
298	Cb3 ghtsqvvpgd tmqtrhvkny hsrsestien flcrsacvyf teykn.....
299	E ...spi.gaf tvks...... gs.lesgfap .fsngtc.pn sviltpgpqf
300
301	---------------------------------------------------
302	PIR format
303	This is NBRF-PIR MAILSERVER version 1.45
304	Command-> get PIR3:A31391
305	\\\
306	ENTRY A31391 #Type Protein
307	TITLE *Esterase-6 - Fruit fly (Drosophila melanogaster)
308
309	DATE 03-Aug-1992 #Sequence 03-Aug-1992 #Text 03-Aug-1992
310	PLACEMENT 0.0 0.0 0.0 0.0 0.0
311	COMMENT *This entry is not verified.
312	SOURCE Drosophila melanogaster
313
314	REFERENCE
315	#Authors Cooke P.H., Oakeshott J.G.
316	#Citation submitted to GenBank, April 1989
317	#Reference-number A31391
318	#Accession A31391
319	#Cross-reference GB:J04167
320
321	SUMMARY #Molecular-weight 61125 #Length 544 #Checksum 1679
322	SEQUENCE
323	5 10 15 20 25 30
324	1 M N Y V G L G L I I V L S C L W L G S N A S D T D D P L L V
325	31 Q L P Q G K L R G R D N G S Y Y S Y E S I P Y A E P P T G D
326	61 L R F E A P E P Y K Q K W S D I F D A T K T P V A C L Q W D
327	91 Q F T P G A N K L V G E E D C L T V S V Y K P K N S K R N S
328	121 F P V V A H I H G G A F M F G A A W Q N G H E N V M R E G K
329	151 F I L V K I S Y R L G P L G F V S T G D R D L P G N Y G L K
330	181 D Q R L A L K W I K Q N I A S F G G E P Q N V L L V G H S A
331	211 G G A S V H L Q M L R E D F G Q L A R A A F S F S G N A L D
332	241 P W V I Q K G A R G R A F E L G R N V G C E S A E D S T S L
333	271 K K C L K S K P A S E L V T A V R K F L I F S Y V P F A P F
334	301 S P V L E P S D A P D A I I T Q D P R D V I K S G K F G Q V
335	331 P W A V S Y V T E D G G Y N A A L L L K E R K S G I V I D D
336	361 L N E R W L E L A P Y L L F Y R D T K T K K D M D D Y S R K
337	391 I K Q E Y I G N Q R F D I E S Y S E L Q R L F T D I L F K N
338	421 S T Q E S L D L H R K Y G K S P A Y A Y V Y D N P A E K G I
339	451 A Q V L A N R T D Y D F G T V H G D D Y F L I F E N F V R D
340	481 V E M R P D E Q I I S R N F I N M L A D F A S S D N G S L K
341	511 Y G E C D F K D N V G S E K F Q L L A I Y I D G C Q N R Q H
342	541 V E F P
343	///
344	\\\
345	---------------------------------------------------
346	PAUP format:
347	The NEXUS Format
348
349	Every block starts with "BEGIN blockname;" and ends with "END;".
350	Each block is composed of one or more statements, each
351	terminated by a semicolon (;).
352
353	Comments may be included in NEXUS files by enclosing them within
354	square brackets, as in "[This is a comment]."
355
356	NEXUS-conforming files are identified by a "#NEXUS" directive at
357	the very beginning of the file (line 1, column 1). If the
358	#NEXUS is omitted PAUP issues a warning but continues
359	processing.
360
361	NEXUS files are entirely free-format. Blanks, tabs, and
362	newlines may be placed anywhere in the file. Unless RESPECTCASE
363	is requested, commands and data may be entered in upper case,
364	lower case, or a mixture of upper and lower case.
365
366	The following conventions are used in the syntax descriptions of
367	the various blocks. Upper-case items are entered exactly as
368	shown. Lower-case items inside of angle brackets -- e.g., <x>
369	-- represent items to be substituted by the user. Items inside
370	of square brackets -- e.g., [X] -- are optional. Items inside
371	of curly braces and separated by vertical bars -- e.g., { X \| Y
372	\| Z } -- are mutually exclusive options.
373
374
375	The DATA Block
376
377	The DATA block contains the data matrix and other associated
378	information. Its syntax is:
379
380	BEGIN DATA;
381	DIMENSIONS NTAX=<number of taxa> NCHAR=<number of characters>;
382	[ FORMAT [ MISSING=<missing-symbol> ]
383	[ LABELPOS={ LEFT \| RIGHT } ]
384	[ SYMBOLS="<symbols-list>" ]
385	[ INTERLEAVE ]
386	[ MATCHCHAR=<match-symbol> ]
387	[ EQUATE="<symbol>=<expansion> [<symbol>=<expansion>...]" ]
388	[ TRANSPOSE ]
389	[ RESPECTCASE ]
390	[ DATATYPE = { STANDARD \| DNA \| RNA \| PROTEIN } ]; ]
391	[ OPTIONS [ IGNORE={ INVAR \| UNINFORM } ]
392	[ MSTAXA = { UNCERTAIN \| POLYMORPH \| VARIABLE } ]
393	[ ZAP = "<list of zapped characters>" ] ; ]
394	[ CHARLABELS <label_1> <label_2> <label_NCHAR> ; ]
395	[ TAXLABELS <label1_1> <label1_2> <label1_NTAX> ; ]
396	[ STATELABELS <currently ignored by PAUP> ; ]
397	MATRIX <data-matrix> ;
398	END;
399
400	--- example PAUP file
401
402	#NEXUS
403
404	[!Brown et al. (1982) primate mitochondrial DNA]
405
406	begin data;
407	dimensions ntax=5 nchar=896;
408	format datatype=dna matchchar=. interleave missing='-';
409	matrix
410	[ 2 4 6 8 ]
411	[ 1 1 1 1 1 ]
412	human aagcttcaccggcgcagtca ttctcataatcgcccacggR cttacatcctcattactatt ctgcctagcaaactcaaact acgaacgcactcacagtcgc
413	chimp ................a.t. .c.................a ...............t.... ..................t. .t........c.........
414	gorilla ..................tg ....t.....t........a ........a......t.... .................... .......a..c.....c...
415	orang ................ac.. cc.....g..t.....t..a ..c........cc....g.. .................... .......a..c.....c...
416	gibbon ......t..a..t...ac.g .c.................a ..a..c..t..cc.g..... ......t............. .......a........c...
417
418	[ 8 8 8 8 8 8 ]
419	[ 0 2 4 6 8 9 ]
420	[ 1 1 1 1 1 6 ]
421	human cttccccacaacaatattca tgtgcctagaccaagaagtt attatctcgaactgacactg agccacaacccaaacaaccc agctctccctaagctt
422	chimp t................... .a................c. ........a.....g..... ...a................ ................
423	gorilla ..................tc .a................c. ........a.g......... ...a.............tt. .a..............
424	orang ta....a...........t. .c.......ga......acc ..cg..a.a......tg... .a.a..c.....g...cta. .a.....a........
425	gibbon a..t.......t........ ....ac...........acc .....t..a........... .a.tg..........gctag .a..............
426	;
427	end;
428	---------------------------------------------------
429
430
431
432
433
434
435	\|\|\|\|\|\|\|\|\|\|\| Sample SMTP mail header
436	---------------------------------------------------
437
438	- - - - - - - - -
439	From GenBank-Retrieval-System@genbank.bio.net Sun Nov 10 17:28:56 1991
440	Received: from genbank.bio.net by sunflower.bio.indiana.edu
441	(4.1/9.5jsm) id AA19328; Sun, 10 Nov 91 17:28:55 EST
442	Received: by genbank.bio.net (5.65/IG-2.0)
443	id AA14458; Sun, 10 Nov 91 14:30:03 -0800
444	Date: Sun, 10 Nov 91 14:30:03 -0800
445	Message-Id: <9111102230.AA14458@genbank.bio.net>
446	From: Database Server <GenBank-Retrieval-System@genbank.bio.net>
447	To: gilbertd@sunflower.bio.indiana.edu
448	Subject: Results of Query for drorna
449	Status: R
450
451	No matches on drorna.
452	- - - - - -
453	From GenBank-Retrieval-System@genbank.bio.net Sun Nov 10 17:28:49 1991
454	Received: from genbank.bio.net by sunflower.bio.indiana.edu
455	(4.1/9.5jsm) id AA19323; Sun, 10 Nov 91 17:28:47 EST
456	Received: by genbank.bio.net (5.65/IG-2.0)
457	id AA14461; Sun, 10 Nov 91 14:30:03 -0800
458	Date: Sun, 10 Nov 91 14:30:03 -0800
459	Message-Id: <9111102230.AA14461@genbank.bio.net>
460	From: Database Server <GenBank-Retrieval-System@genbank.bio.net>
461	To: gilbertd@sunflower.bio.indiana.edu
462	Subject: Results of Query for droest6
463	Status: R
464
465	LOCUS DROEST6 1819 bp ss-mRNA INV 31-AUG-1987
466	DEFINITION D.melanogaster esterase-6 mRNA, complete cds.
467	ACCESSION M15961
468
469
470
471
472
473
474
475
476
477
478
479
480	\|\|\|\|\|\|\|\|\|\|\| GCG manual discussion of sequence symbols:
481	---------------------------------------------------
482
483	III_SEQUENCE_SYMBOLS
484
485
486	GCG programs allow all upper and lower case letters, periods (.),
487	asterisks (*), pluses (+), ampersands (&), and ats (@) as symbols in
488	biological sequences. Nucleotide symbols, their complements, and the
489	standard one-letter amino acid symbols are shown below in separate lists.
490	The meanings of the symbols +, &, and @ have not been assigned at this
491	writing (March, 1989).
492
493	GCG uses the letter codes for amino acid codes and nucleotide
494	ambiguity proposed by IUB (Nomenclature Committee, 1985,
495	Eur. J. Biochem. 150; 1-5). These codes are compatible with the codes
496	used by the EMBL, GenBank, and NBRF data libraries.
497
498
499	NUCLEOTIDES
500
501	The meaning of each symbol, its complement, and the Cambridge and
502	Stanford equivalents are shown below. Cambridge files can be converted
503	into GCG files and vice versa with the programs FROMSTADEN and TOSTADEN.
504	IntelliGenetics sequence files can be interconverted with the programs
505	FROMIG and TOIG.
506
507	IUB/GCG Meaning Complement Staden/Sanger Stanford
508
509	A A T A A
510	C C G C C
511	G G C G G
512	T/U T A T T/U
513	M A or C K 5 J
514	R A or G Y R R
515	W A or T W 7 L
516	S C or G S 8 M
517	Y C or T R Y Y
518	K G or T M 6 K
519	V A or C or G B not supported N
520	H A or C or T D not supported N
521	D A or G or T H not supported N
522	B C or G or T V not supported N
523	X/N G or A or T or C X -/X N
524	. not G or A or T or C . not supported ?
525
526
527	The frame ambiguity codes used by Staden are not supported by GCG
528	and are translated by FROMSTADEN as the lower case single base
529	equivalent.
530
531	Staden Code Meaning GCG
532
533	D C or CC c
534	V T or TT t
535	B A or AA a
536	H G or GG g
537	K C or CX c
538	L T or TX t
539	M A or AX a
540	N G or GX g
541
542
543	AMINO ACIDS
544
545	Here is a list of the standard one-letter amino acid codes and their
546	three-letter equivalents. The synonymous codons and their depiction in
547	the IUB codes are shown. You should recognize that the codons following
548	semicolons (;) are not sufficiently specific to define a single amino
549	acid even though they represent the best possible back translation into
550	the IUB codes! All of the relationships in this list can be redefined by
551	the user in a local data file described below.
552
553	IUB
554	Symbol 3-letter Meaning Codons Depiction
555	A Ala Alanine GCT,GCC,GCA,GCG !GCX
556	B Asp,Asn Aspartic,
557	Asparagine GAT,GAC,AAT,AAC !RAY
558	C Cys Cysteine TGT,TGC !TGY
559	D Asp Aspartic GAT,GAC !GAY
560	E Glu Glutamic GAA,GAG !GAR
561	F Phe Phenylalanine TTT,TTC !TTY
562	G Gly Glycine GGT,GGC,GGA,GGG !GGX
563	H His Histidine CAT,CAC !CAY
564	I Ile Isoleucine ATT,ATC,ATA !ATH
565	K Lys Lysine AAA,AAG !AAR
566	L Leu Leucine TTG,TTA,CTT,CTC,CTA,CTG
567	!TTR,CTX,YTR;YTX
568	M Met Methionine ATG !ATG
569	N Asn Asparagine AAT,AAC !AAY
570	P Pro Proline CCT,CCC,CCA,CCG !CCX
571	Q Gln Glutamine CAA,CAG !CAR
572	R Arg Arginine CGT,CGC,CGA,CGG,AGA,AGG
573	!CGX,AGR,MGR;MGX
574	S Ser Serine TCT,TCC,TCA,TCG,AGT,AGC !TCX,AGY;WSX
575	T Thr Threonine ACT,ACC,ACA,ACG !ACX
576	V Val Valine GTT,GTC,GTA,GTG !GTX
577	W Trp Tryptophan TGG !TGG
578	X Xxx Unknown !XXX
579	Y Tyr Tyrosine TAT, TAC !TAY
580	Z Glu,Gln Glutamic,
581	Glutamine GAA,GAG,CAA,CAG !SAR
582	* End Terminator TAA, TAG, TGA !TAR,TRA;TRR
583
584
585
586
587
588
589
590
591	\|\|\|\|\|\|\|\|\|\|\| docs from PSC on sequence formats:
592	---------------------------------------------------
593
594
595	Nucleic Acid and Protein Sequence File Formats
596
597
598	It will probably save you some time if you have your data in a usable
599	format before you send it to us. However, we do have the University of
600	Wisconsin Genetics Computing Group programs running on our VAXen and
601	this package includes several reformatting utilities. Our programs
602	usually recognize any of several standard formats, including GenBank,
603	EMBL, NBRF, and MolGen/Stanford. For the purposes of annotating an
604	analysis we find the GenBank and EMBL formats most useful, particularly
605	if you have already received an accession number from one of these
606	organizations for your sequence.
607
608	Our programs do not require that all of the line types available in
609	GenBank, EMBL, or NBRF file formats be present for the file format to
610	be recognized and processed. The following pages outline the essential
611	details required for correct processing of files by our programs.
612	Additional information may be present but will generally be ignored.
613
614
615	GenBank File Format
616
617	File Header
618
619	1. The first line in the file must have "GENETIC SEQUENCE DATA BANK"
620	in spaces 20 through 46 (see LINE 1, below).
621	2. The next 8 lines may contain arbitrary text. They are ignored but
622	are required to maintain the GenBank format (see LINE 2 - LINE 9).
623
624	Sequence Data Entries
625
626	3. Each sequence entry in the file should have the following format.
627	a) first line: Must have LOCUS in the first 5 spaces. The
628	genetic locus name or identifier must be in spaces
629	13 - 22. The length of the sequences is right
630	justified in spaces 23 through 29 (see LINE 10).
631	b) second line: Must have DEFINITION in the first 10 spaces.
632	Spaces 13 - 80 are free form text to identify the
633	sequence (see LINE 11).
634	c) third line: Must have ACCESSION in the first 9 spaces. Spaces
635	13 - 18 must hold the primary accession number
636	(see LINE 12).
637	d) fourth line: Must have ORIGIN in the first 6 spaces. Nothing
638	else is required on this line, it indicates that
639	the nucleic acid sequence begins on the next line
640	(see LINE 13).
641	e) fifth line: Begins the nucleotide sequence. The first 9
642	spaces of each sequence line may either be blank
643	or may contain the position in the sequence of the
644	first nucleotide on the line. The next 66 spaces
645	hold the nucleotide sequence in six blocks of ten
646	nucleotides. Each of the six blocks begins with a
647	blank space followed by ten nucleotides. Thus the
648	first nucleotide is in space eleven of the line while
649	the last is in space 75 (see LINE 14, LINE 15).
650	f) last line: Must have // in the first 2 spaces to indicate
651	termination of the sequence (see LINE 16).
652
653	NOTE: Multiple sequences may appear in each file. To begin another
654	sequence go back to a) and start again.
655
656
657	Example GenBank file
658
659
660	LINE 1 : GENETIC SEQUENCE DATA BANK
661	LINE 2 :
662	LINE 3 :
663	LINE 4 :
664	LINE 5 :
665	LINE 6 :
666	LINE 7 :
667	LINE 8 :
668	LINE 9 :
669	LINE 10 :LOCUS L_Name Length BP
670	LINE 11 :DEFINITION Describe the sequence any way you want
671	LINE 12 :ACCESSION Accession Number
672	LINE 13 :ORIGIN
673	LINE 14 : 1 acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt a...
674	LINE 15 : 61 acgt...
675	LINE 16 ://
676
677
678
679	EMBL File Format
680
681	Unlike the GenBank file format the EMBL file format does not require
682	a series of header lines. Thus the first line in the file begins
683	the first sequence entry of the file.
684
685	1. The first line of each sequence entry contains the two letters ID
686	in the first two spaces. This is followed by the EMBL identifier
687	in spaces 6 through 14. (See LINE 1).
688
689	2. The second line of each sequence entry has the two letters AC in
690	the first two spaces. This is followed by the accession number in
691	spaces 6 through 11. (See LINE 2).
692
693	3. The third line of each sequence entry has the two letters DE in the
694	first two spaces. This is followed by a free form text definition
695	in spaces 6 through 72. (See LINE 3).
696
697	4. The fourth line in each sequence entry has the two letters SQ in
698	the first two spaces. This is followed by the length of the
699	sequence beginning at or after space 13. After the sequence length
700	there is a blank space and the two letters BP. (See LINE 4).
701
702	5. The nucleotide sequence begins on the fifth line of the sequence
703	entry. Each line of sequence begins with four blank spaces. The
704	next 66 spaces hold the nucleotide sequence in six blocks of ten
705	nucleotides. Each of the six blocks begins with a blank space
706	followed by ten nucleotides. Thus the first nucleotide is in space
707	6 of the line while the last is in space 70. (See LINE 5 -
708	LINE 6).
709
710	6. The last line of each sequence entry in the file is a terminator
711	line which has the two characters // in the first two spaces.
712	(See LINE 7).
713
714	7. Multiple sequences may appear in each file. To begin another
715	sequence go back to item 1 and start again.
716
717
718	Example EMBL file
719
720	LINE 1 :ID ID_name
721	LINE 2 :AC Accession number
722	LINE 3 :DE Describe the sequence any way you want
723	LINE 4 :SQ Length BP
724	LINE 5 : ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTA...
725	LINE 6 : ACGT...
726	LINE 7 ://
727
728
729
730	NBRF (protein or nucleic acid) File Format
731
732	1. The first line of each sequence entry begins with a greater than
733	symbol, >. This is immediately followed by the two character
734	sequence type specifier. Space four must contain a semi-colon.
735	Beginning in space five is the sequence name or identification code
736	for the NBRF database. The code is from four to six letters and
737	numbers. (See LINE 1).
738
739	!!!! >> add these to readseq
740	Specifier Sequence type
741
742	P1 protein, complete
743	F1 protein, fragment
744	DL DNA, linear
745	DC DNA, circular
746	RL RNA, linear
747	RC RNA, circular
748	N1 functional RNA, other than tRNA
749	N3 tRNA
750
751	2. The second line of each sequence entry contains two kinds of
752	information. First is the sequence name which is separated from
753	the organism or organelle name by the three character sequence
754	blank space, dash, blank space, " - ". There is no special
755	character marking the beginning of this line. (See LINE 2).
756
757	3. Either the amino acid or nucleic acid sequence begins on line three
758	and can begin in any space, including the first. The sequence is
759	free format and may be interrupted by blanks for ease of reading.
760	Protein sequences man contain special punctuation to indicate
761	various indeterminacies in the sequence. In the NBRF data files
762	all lines may be up to 500 characters long. However some PSC
763	programs currently have a limit of 130 characters per line
764	(including blanks), and BitNet will not accept lines of over eighty
765	characters. (See LINE 3, LINE 4, and LINE 5).
766
767	The last character in the sequence must be an asterisks, *.
768
769	Example NBRF file
770
771	LINE 1 :>P1;CBRT
772	LINE 2 :Cytochrome b - Rat mitochondrion (SGC1)
773	LINE 3 :M T N I R K S H P L F K I I N H S F I D L P A P S
774	LINE 4 : VTHICRDVN Y GWL IRY
775	LINE 5 :TWIGGQPVEHPFIIIGQLASISYFSIILILMPISGIVEDKMLKWN*
776
777
778
779	MolGen/Stanford File Format
780
781	1. The first line in a sequence file is a comment line. This line
782	begins with a semi-colon in the first space. This line need
783	not be present. If it is present it holds descriptive text.
784	There may be as many comment lines as desired at the first of
785	sequence file. (See LINE 1).
786
787	2. The second line must be present and contains an identifier or
788	name for the sequence in the first ten spaces. (See LINE 2).
789
790	3. The sequence begins on the third line and occupies up to eighty
791	spaces. Spaces may be included in the sequence for ease of
792	reading. The sequence continues for as many line as needed
793	and is terminated with a 1 or 2. 1 indicates a linear sequence
794	while 2 marks a circular sequence. (See LINE 3 and LINE 4).
795
796	Example MolGen/Stanford file
797
798	LINE 1 :; Describe the sequence any way you want
799	LINE 2 :ECTRNAGLY2
800	LINE 3 :ACGCACGTAC ACGTACGTAC A C G T C C G T ACG TAC GTA CGT
801	LINE 4 : GCTTA GG G C T A1
802
803
804
805
806	\|\|\|\|\|\|\|\|\|\|\| Phylip file format
807	---------------------------------------------------
808
809	Phylip 3.3 File Format (DNA sequences)
810
811
812	The input and output formats for PROTPARS and for RESTML are described in
813	their document files. In general their input formats are similar to those
814	described here, except that the one-letter codes for data are specific to those
815	programs and are described in those document files. Since the input formats
816	for the eight DNA sequence programs apply to all eight, they are described
817	here. Their input formats are standard: the data have A's, G's, C's and T's
818	(or U's). The first line of the input file contains the number of species and
819	the number of sites. As with the other programs, options information may
820	follow this. In the case of DNAML, DNAMLK, and DNADIST an additional line
821	(described in the document file for these pograms) may follow the first one.
822	Following this, each species starts on a new line. The first 10 characters of
823	that line are the species name. There then follows the base sequence of that
824	species, each character being one of the letters A, B, C, D, G, H, K, M, N, O,
825	R, S, T, U, V, W, X, Y, ?, or - (a period was also previously allowed but it is
826	no longer allowed, because it sometimes is used to in aligned sequences to mean
827	"the same as the sequence above"). Blanks will be ignored, and so will
828	numerical digits. This allows GENBANK and EMBL sequence entries to be read
829	with minimum editing.
830
831	These characters can be either upper or lower case. The algorithms
832	convert all input characters to upper case (which is how they are treated).
833	The characters constitute the IUPAC (IUB) nucleic acid code plus some slight
834	extensions. They enable input of nucleic acid sequences taking full account of
835	any ambiguities in the sequence.
836
837	The sequences can continue over multiple lines; when this is done the sequences
838	must be either in "interleaved" format, similar to the output of alignment
839	programs, or "sequential" format. These are described in the main document
840	file. In sequential format all of one sequence is given, possibly on multiple
841	lines, before the next starts. In interleaved format the first part of the
842	file should contain the first part of each of the sequences, then possibly a
843	line containing nothing but a carriage-return character, then the second part
844	of each sequence, and so on. Only the first parts of the sequences should be
845	preceded by names. Here is a hypothetical example of interleaved format:
846
847	5 42
848	Turkey AAGCTNGGGC ATTTCAGGGT
849	Salmo gairAAGCCTTGGC AGTGCAGGGT
850	H. SapiensACCGGTTGGC CGTTCAGGGT
851	Chimp AAACCCTTGC CGTTACGCTT
852	Gorilla AAACCCTTGC CGGTACGCTT
853
854	GAGCCCGGGC AATACAGGGT AT
855	GAGCCGTGGC CGGGCACGGT AT
856	ACAGGTTGGC CGTTCAGGGT AA
857	AAACCGAGGC CGGGACACTC AT
858	AAACCATTGC CGGTACGCTT AA
859
860	while in sequential format the same sequences would be:
861
862	5 42
863	Turkey AAGCTNGGGC ATTTCAGGGT
864	GAGCCCGGGC AATACAGGGT AT
865	Salmo gairAAGCCTTGGC AGTGCAGGGT
866	GAGCCGTGGC CGGGCACGGT AT
867	H. SapiensACCGGTTGGC CGTTCAGGGT
868	ACAGGTTGGC CGTTCAGGGT AA
869	Chimp AAACCCTTGC CGTTACGCTT
870	AAACCGAGGC CGGGACACTC AT
871	Gorilla AAACCCTTGC CGGTACGCTT
872	AAACCATTGC CGGTACGCTT AA
873
874
875	Note, of course, that a portion of a sequence like this:
876
877	300 AAGCGTGAAC GTTGTACTAA TRCAG
878
879	is perfectly legal, assuming that the species name has gone before, and is
880	filled out to full length by blanks. The above digits and blanks will be
881	ignored, the sequence being taken as starting at the first base symbol (in this
882	case an A).
883
884	The present versions of the programs may sometimes have difficulties with
885	the blank lines between groups of lines, and if so you might want to retype
886	those lines, making sure that they have only a carriage-return and no blank
887	characters on them, or you may perhaps have to eliminate them. The symptoms of
888	this problem are that the programs complain that the sequences are not properly
889	aligned, and you can find no other cause for this complaint.
890
891	------------------------------------------------
892
893
894	\|\|\|\|\|\|\|\|\|\|\| ASN.1 file format
895	---------------------------------------------------
896
897
898	ASN.1 -- see NCBI toolkit docs, source and examples (ncbi.nlm.nih.gov)
899
900	Example asn.1 sequence file----
901
902	Bioseq-set ::= {
903	seq-set {
904	seq {
905	id { local id 1 } , -- id essential
906	descr { title "Dummy sequence data from nowhere" } , -- optional
907	inst { -- inst essential
908	repr raw ,
909	mol dna ,
910	length 156 ,
911	topology linear ,
912	seq-data
913	iupacna "GAATTCATTTTTGAAACAAATCGACCTGACGACGGAATGGTACTCGAATTA
914	TGGGCCAAAGGGTTTTATGGGACAAATTAATAGGTGTTCATTATATGCCACTTTCGGAGATTAGATACAGCAATGCAG
915	TGGATTCAAAGCAATAGAGTTGTTCTT"
916	} } ,
917
918	seq {
919	id { local id 2 } ,
920	descr { title "Dummy sequence 2 data from somewhere else" } ,
921	inst {
922	repr raw ,
923	mol dna ,
924	length 150 ,
925	topology linear ,
926	seq-data
927	iupacna "TTTTTTTTTTTTGAAACAAATCGACCTGACGACGGAATGGTACTCGAATTA
928	TGGGCCAAAGGGTTTTATGGGACAAATTAATAGGTGTTCATTATATGCCACTTTCGGAGATTAGATACAGCAATGCAG
929	TGGATTCAAAGCAATAGAGTT"
930	}
931	}
932	}
933	}
934
935
936	partial ASN.1 description from toolkit
937
938	Bioseq ::= SEQUENCE {
939	id SET OF Seq-id , -- equivalent identifiers
940	descr Seq-descr OPTIONAL , -- descriptors
941	inst Seq-inst , -- the sequence data
942	annot SET OF Seq-annot OPTIONAL }
943
944	Seq-inst ::= SEQUENCE { -- the sequence data itself
945	repr ENUMERATED { -- representation class
946	not-set (0) , -- empty
947	virtual (1) , -- no seq data
948	raw (2) , -- continuous sequence
949	seg (3) , -- segmented sequence
950	const (4) , -- constructed sequence
951	ref (5) , -- reference to another sequence
952	consen (6) , -- consensus sequence or pattern
953	map (7) , -- ordered map (genetic, restriction)
954	other (255) } ,
955	mol ENUMERATED { -- molecule class in living organism
956	not-set (0) , -- > cdna = rna
957	dna (1) ,
958	rna (2) ,
959	aa (3) ,
960	na (4) , -- just a nucleic acid
961	other (255) } ,
962	length INTEGER OPTIONAL , -- length of sequence in residues
963	fuzz Int-fuzz OPTIONAL , -- length uncertainty
964	topology ENUMERATED { -- topology of molecule
965	not-set (0) ,
966	linear (1) ,
967	circular (2) ,
968	tandem (3) , -- some part of tandem repeat
969	other (255) } DEFAULT linear ,
970	strand ENUMERATED { -- strandedness in living organism
971	not-set (0) ,
972	ss (1) , -- single strand
973	ds (2) , -- double strand
974	mixed (3) ,
975	other (255) } OPTIONAL , -- default ds for DNA, ss for RNA, pept
976	seq-data Seq-data OPTIONAL , -- the sequence
977	ext Seq-ext OPTIONAL , -- extensions for special types
978	hist Seq-hist OPTIONAL } -- sequence history
979
980	------------------------------------------------

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