|
Last change
on this file was
2,
checked in by oldcode, 24 years ago
|
|
Initial revision
|
-
Property svn:eol-style set to
native
-
Property svn:keywords set to
Author Date Id Revision
|
|
File size:
3.1 KB
|
| Line | |
|---|
| 1 | arb_item:Clustalv Alignment (DNA) |
|---|
| 2 | itemmethod:(tr '"%//' '>' <in1 >clus_in; RUN_IN_WINDOW((clustalv /output=PIR /infile=clus_in /align /ktuple=$KTUP /window=$WIN $Trans /fixedgap=$FIXED /floatgap=$FLOAT;cat clus_in.pir |sed "s/^>DL;/#/g" |sed "s/^>P1;/%/g" |sed "s/^\*$//g" >out1; )); /bin/rm -f clus_in* in1) |
|---|
| 3 | |
|---|
| 4 | itemhelp:clustal_help |
|---|
| 5 | |
|---|
| 6 | arg:KTUP |
|---|
| 7 | argtype:slider |
|---|
| 8 | arglabel:K-tuple size for fast pairwise search |
|---|
| 9 | argmin:1 |
|---|
| 10 | argmax:10 |
|---|
| 11 | argvalue:2 |
|---|
| 12 | |
|---|
| 13 | arg:WIN |
|---|
| 14 | argtype:slider |
|---|
| 15 | arglabel:Window size |
|---|
| 16 | argmin:1 |
|---|
| 17 | argmax:10 |
|---|
| 18 | argvalue:4 |
|---|
| 19 | |
|---|
| 20 | arg:Trans |
|---|
| 21 | argtype:chooser |
|---|
| 22 | arglabel:Transitions weighted? |
|---|
| 23 | argchoice:Yes:/TRANSIT |
|---|
| 24 | argchoice:No: |
|---|
| 25 | |
|---|
| 26 | arg:FIXED |
|---|
| 27 | argtype:slider |
|---|
| 28 | arglabel:Fixed gap penalty |
|---|
| 29 | argmin:1 |
|---|
| 30 | argmax:100 |
|---|
| 31 | argvalue:10 |
|---|
| 32 | |
|---|
| 33 | arg:FLOAT |
|---|
| 34 | arglabel:Floating gap penalty |
|---|
| 35 | argtype:slider |
|---|
| 36 | argmin:1 |
|---|
| 37 | argmax:100 |
|---|
| 38 | argvalue:10 |
|---|
| 39 | |
|---|
| 40 | in:in1 |
|---|
| 41 | informat:flat |
|---|
| 42 | insave: |
|---|
| 43 | |
|---|
| 44 | out:out1 |
|---|
| 45 | outformat:flat |
|---|
| 46 | |
|---|
| 47 | |
|---|
| 48 | item:Clustalw DNA Alignment |
|---|
| 49 | itemmethod:(tr '"%//' '>' <in1 >clus_in;RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align -ktuple=$KTUP_ -window=$WIN_ -topdiags=$WIN_ $MATRIX_ -gapopen=$FIXED_ -gapext=$FLOAT_ -transweight=0.5 -type=DNA -DNAMATRIX=$MATRIX_;cat clus_in.pir |sed "s/^>DL;/#/g" |sed "s/^>P1;/%/g" |sed "s/^\*$//g" >out1; )); /bin/rm -f clus_in* in1) |
|---|
| 50 | |
|---|
| 51 | itemhelp:clustal.help |
|---|
| 52 | |
|---|
| 53 | arg:KTUP |
|---|
| 54 | argtype:slider |
|---|
| 55 | arglabel:K-tuple size for fast pairwise search |
|---|
| 56 | argmin:1 |
|---|
| 57 | argmax:10 |
|---|
| 58 | argvalue:2 |
|---|
| 59 | |
|---|
| 60 | arg:WIN |
|---|
| 61 | argtype:slider |
|---|
| 62 | arglabel:Window size for fast pairwise search |
|---|
| 63 | argmin:1 |
|---|
| 64 | argmax:10 |
|---|
| 65 | argvalue:4 |
|---|
| 66 | |
|---|
| 67 | arg:MATRIX_ |
|---|
| 68 | argtype:chooser |
|---|
| 69 | arglabel:Weighting matrix |
|---|
| 70 | argchoice:BLOSUM:BLOSUM |
|---|
| 71 | argchoice:PAM:PAM |
|---|
| 72 | argchoice:GONNET:GONNET |
|---|
| 73 | argchoice:ID:ID |
|---|
| 74 | |
|---|
| 75 | arg:FIXED_ |
|---|
| 76 | argtype:slider |
|---|
| 77 | arglabel:Gap Open Panelty |
|---|
| 78 | argmin:1 |
|---|
| 79 | argmax:100 |
|---|
| 80 | argvalue:8.7 |
|---|
| 81 | |
|---|
| 82 | arg:FLOAT_ |
|---|
| 83 | arglabel:Gap Extend Panelty |
|---|
| 84 | argtype:slider |
|---|
| 85 | argmin:.001 |
|---|
| 86 | argmax:1 |
|---|
| 87 | argvalue:.1 |
|---|
| 88 | |
|---|
| 89 | |
|---|
| 90 | in:in1 |
|---|
| 91 | informat:flat |
|---|
| 92 | insave: |
|---|
| 93 | |
|---|
| 94 | out:out1 |
|---|
| 95 | outformat:flat |
|---|
| 96 | |
|---|
| 97 | |
|---|
| 98 | item:Clustalw Protein Alignment |
|---|
| 99 | itemmethod:(tr '"%//' '>' <in1 >clus_in;RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align -ktuple=$KTUP_ -window=$WIN_ -topdiags=$WIN_ $MATRIX_ -gapopen=$FIXED_ -gapext=$FLOAT_ -type=PROTEIN;cat clus_in.pir |sed "s/^>DL;/#/g" |sed "s/^>P1;/%/g" |sed "s/^\*$//g" >out1; ));\/bin/rm -f clus_in* in1) |
|---|
| 100 | |
|---|
| 101 | |
|---|
| 102 | itemhelp:clustalw.help |
|---|
| 103 | |
|---|
| 104 | arg:KTUP_ |
|---|
| 105 | argtype:slider |
|---|
| 106 | arglabel:K-tuple size for fast pairwise search |
|---|
| 107 | argmin:1 |
|---|
| 108 | argmax:10 |
|---|
| 109 | argvalue:2 |
|---|
| 110 | |
|---|
| 111 | arg:WIN_ |
|---|
| 112 | argtype:slider |
|---|
| 113 | arglabel:Window size and top diagonals for fast alignment |
|---|
| 114 | argmin:1 |
|---|
| 115 | argmax:10 |
|---|
| 116 | argvalue:4 |
|---|
| 117 | |
|---|
| 118 | arg:MATRIX_ |
|---|
| 119 | argtype:chooser |
|---|
| 120 | arglabel:Weighting matrix |
|---|
| 121 | argchoice:BLOSUM:BLOSUM |
|---|
| 122 | argchoice:PAM:PAM |
|---|
| 123 | argchoice:GONNET:GONNET |
|---|
| 124 | argchoice:ID:ID |
|---|
| 125 | |
|---|
| 126 | arg:FIXED_ |
|---|
| 127 | argtype:slider |
|---|
| 128 | arglabel:Gap Open Panelty |
|---|
| 129 | argmin:1 |
|---|
| 130 | argmax:100 |
|---|
| 131 | argvalue:8.7 |
|---|
| 132 | |
|---|
| 133 | arg:FLOAT_ |
|---|
| 134 | arglabel:Gap Extend Panelty |
|---|
| 135 | argtype:slider |
|---|
| 136 | argmin:.001 |
|---|
| 137 | argmax:1 |
|---|
| 138 | argvalue:.1 |
|---|
| 139 | |
|---|
| 140 | |
|---|
| 141 | |
|---|
| 142 | in:in1 |
|---|
| 143 | informat:flat |
|---|
| 144 | insave: |
|---|
| 145 | |
|---|
| 146 | out:out1 |
|---|
| 147 | outformat:flat |
|---|
| 148 | |
|---|
| 149 | item:Assemble Contigs |
|---|
| 150 | itemmethod: (tr '"%//' '>' <in1 >in1.tmp;CAP2 in1.tmp $OVERLAP $PMATCH > out1;/bin/rm -f in1.tmp) |
|---|
| 151 | itemhelp:CAP2.help |
|---|
| 152 | |
|---|
| 153 | arg:OVERLAP |
|---|
| 154 | argtype:slider |
|---|
| 155 | arglabel:Minimum overlap? |
|---|
| 156 | argmin:5 |
|---|
| 157 | argmax:100 |
|---|
| 158 | argvalue:20 |
|---|
| 159 | |
|---|
| 160 | arg:PMATCH |
|---|
| 161 | argtype:slider |
|---|
| 162 | arglabel:Percent match required within overlap |
|---|
| 163 | argmin:25 |
|---|
| 164 | argmax:100 |
|---|
| 165 | argvalue:90 |
|---|
| 166 | |
|---|
| 167 | in:in1 |
|---|
| 168 | informat:flat |
|---|
| 169 | |
|---|
| 170 | out:out1 |
|---|
| 171 | outformat:gde |
|---|
| 172 | |
|---|
Note: See
TracBrowser
for help on using the repository browser.
