source: branches/profile/GDEHELP/HELP_PLAIN/CAP2.help

 CONTIG ASSEMBLY PROGRAM (CAP)

   copyright (c) 1991  Xiaoqiu Huang

   The distribution of the program is granted provided no charge
   is made and the copyright notice is included.

   Proper attribution of the author as the source of the software
   would be appreciated:

   "A Contig Assembly Program Based on Sensitive Detection of
   Fragment Overlaps" (submitted to Genomics, 1991)

        Xiaoqiu Huang
        Department of Computer Science
        Michigan Technological University
        Houghton, MI 49931
        E-mail:  huang@cs.mtu.edu

   The CAP program uses a dynamic programming algorithm to compute
   the maximal-scoring overlapping alignment between two fragments.
   Fragments in random orientations are assembled into contigs by a
   greedy approach in order of the overlap scores. CAP is efficient
   in computer memory: a large number of arbitrarily long fragments
   can be assembled. The time requirement is acceptable; for example,
   CAP took 4 hours to assemble 1015 fragments of a total of 252 kb
   nucleotides on a Sun SPARCstation SLC. The program is written in C
   and runs on Sun workstations.

   Below is a description of the parameters in the #define section of CAP.
   Two specially chosen sets of substitution scores and indel penalties
   are used by the dynamic programming algorithm: heavy set for regions
   of low sequencing error rates and light set for fragment ends of high
   sequencing error rates. (Use integers only.)

        Heavy set:                       Light set:

        MATCH     =  2                   MATCH     =  2
        MISMAT    = -6                   LTMISM    = -3
        EXTEND    =  4                   LTEXTEN   =  2

    In the initial assembly, any overlap must be of length at least OVERLEN,
    and any overlap/containment must be of identity percentage at least
    PERCENT. After the initial assembly, the program attempts to join
    contigs together using weak overlaps. Two contigs are merged if the
    score of the overlapping alignment is at least CUTOFF. The value for
    CUTOFF is chosen according to the value for MATCH.

    DELTA is a parameter in necessary conditions for overlap/containment.
    Those conditions are used to quickly reject pairs of fragments that
    could not possibly have an overlap/containment relationship.
    The dynamic programming algorithm is only applied to pairs of fragments
    that pass the screening. A large value for DELTA means stringent
    conditions, where the value for DELTA is a real number at least 8.0.

    POS5 and POS3 are fragment positions such that the 5' end between base 1
    and base POS5, and the 3' end after base POS3 are of high sequencing
    error rates, say more than 5%. For mismatches and indels occurring in
    the two ends, light penalties are used.

    A file of input fragments looks like:

      |  >G019uabh
      |  ATACATCATAACACTACTTCCTACCCATAAGCTCCTTTTAACTTGTTAAA
      |  GTCTTGCTTGAATTAAAGACTTGTTTAAACACAAAAATTTAGAGTTTTAC
      |  TCAACAAAAGTGATTGATTGATTGATTGATTGATTGATGGTTTACAGTAG
      |  GACTTCATTCTAGTCATTATAGCTGCTGGCAGTATAACTGGCCAGCCTTT
      |  AATACATTGCTGCTTAGAGTCAAAGCATGTACTTAGAGTTGGTATGATTT
      |  ATCTTTTTGGTCTTCTATAGCCTCCTTCCCCATCCCCATCAGTCTTAATC
      |  AGTCTTGTTACGTTATGACTAATCTTTGGGGATTGTGCAGAATGTTATTT
      |  TAGATAAGCAAAACGAGCAAAATGGGGAGTTACTTATATTTCTTTAAAGC
      |  >G028uaah
      |  CATAAGCTCCTTTTAACTTGTTAAAGTCTTGCTTGAATTAAAGACTTGTT
      |  TAAACACAAAATTTAGACTTTTACTCAACAAAAGTGATTGATTGATTGAT
      |  TGATTGATTGATGGTTTACAGTAGGACTTCATTCTAGTCATTATAGCTGC
      |  TGGCAGTATAACTGGCCAGCCTTTAATACATTGCTGCTTAGAGTCAAAGC
      |  ATGTACTTAGAGTTGGTATGATTTATCTTTTTGGTCTTCTATAGCCTCCT
      |  TCCCCATCCCATCAGTCT
      |  >G022uabh
      |  TATTTTAGAGACCCAAGTTTTTGACCTTTTCCATGTTTACATCAATCCTG
      |  TAGGTGATTGGGCAGCCATTTAAGTATTATTATAGACATTTTCACTATCC
      |  CATTAAAACCCTTTATGCCCATACATCATAACACTACTTCCTACCCATAA
      |  GCTCCTTTTAACTTGTTAAAGTCTTGCTTGAATTAAAGACTTGTTTAAAC
      |  ACAAAATTTAGACTTTTACTCAACAAAAGTGATTGATTGATTGATTGATT
      |  GATTGAT
      |  >G023uabh
      |  AATAAATACCAAAAAAATAGTATATCTACATAGAATTTCACATAAAATAA
      |  ACTGTTTTCTATGTGAAAATTAACCTAAAAATATGCTTTGCTTATGTTTA
      |  AGATGTCATGCTTTTTATCAGTTGAGGAGTTCAGCTTAATAATCCTCTAC
      |  GATCTTAAACAAATAGGAAAAAAACTAAAAGTAGAAAATGGAAATAAAAT
      |  GTCAAAGCATTTCTACCACTCAGAATTGATCTTATAACATGAAATGCTTT
      |  TTAAAAGAAAATATTAAAGTTAAACTCCCCTATTTTGCTCGTTTTTGCTT
      |  ATCTAAAATACATTCTGCACAATCCCCAAAGATTGATCATACGTTAC
      |  >G006uaah
      |  ACATAAAATAAACTGTTTTCTATGTGAAAATTAACCTANNATATGCTTTG
      |  CTTATGTTTAAGATGTCATGCTTTTTATCAGTTGAGGAGTTCAGCTTAAT
      |  AATCCTCTAAGATCTTAAACAAATAGGAAAAAAACTAAAAGTAGAAAATG
      |  GAAATAAAATGTCAAAGCATTTCTACCACTCAGAATTGATCTTATAACAT
      |  GAAATGCTTTTTAAAAGAAAATATTAAAGTTAAACTCCCC

   A string after ">" is the name of the following fragment.
   Only the five upper-case letters A, C, G, T and N are allowed
   to appear in fragment data. No other characters are allowed.
   A common mistake is the use of lower case letters in a fragment.

   To run the program, type a command of form

        cap  file_of_fragments

   The output goes to the terminal screen. So redirection of the
   output into a file is necessary. The output consists of three parts:
   overview of contigs at fragment level, detailed display of contigs
   at nucleotide level, and consensus sequences.
   '+' = direct orientation; '-' = reverse complement
   The output of CAP on the sample input data looks like:

      |  #Contig 1
      |  
      |  #G022uabh+(0)
      |  TATTTTAGAGACCCAAGTTTTTGACCTTTTCCATGTTTACATCAATCCTGTAGGTGATTG
      |  GGCAGCCATTTAAGTATTATTATAGACATTTTCACTATCCCATTAAAACCCTTTATGCCC
      |  ATACATCATAACACTACTTCCTACCCATAAGCTCCTTTTAACTTGTTAAAGTCTTGCTTG
      |  AATTAAAGACTTGTTTAAACACAAAA-TTTAGACTTTTACTCAACAAAAGTGATTGATTG
      |  ATTGATTGATTGATTGAT
      |  #G028uaah+(145)
      |  CATAAGCTCCTTTTAACTTGTTAAAGTCTTGCTTGAATTAAAGACTTGTTTAAACACAAA
      |  A-TTTAGACTTTTACTCAACAAAAGTGATTGATTGATTGATTGATTGATTGATGGTTTAC
      |  AGTAGGACTTCATTCTAGTCATTATAGCTGCTGGCAGTATAACTGGCCAGCCTTTAATAC
      |  ATTGCTGCTTAGAGTCAAAGCATGTACTTAGAGTTGGTATGATTTATCTTTTTGGTCTTC
      |  TATAGCCTCCTTCCCCATCCC-ATCAGTCT
      |  #G019uabh+(120)
      |  ATACATCATAACACTACTTCCTACCCATAAGCTCCTTTTAACTTGTTAAAGTCTTGCTTG
      |  AATTAAAGACTTGTTTAAACACAAAAATTTAGAGTTTTACTCAACAAAAGTGATTGATTG
      |  ATTGATTGATTGATTGATGGTTTACAGTAGGACTTCATTCTAGTCATTATAGCTGCTGGC
      |  AGTATAACTGGCCAGCCTTTAATACATTGCTGCTTAGAGTCAAAGCATGTACTTAGAGTT
      |  GGTATGATTTATCTTTTTGGTCTTCTATAGCCTCCTTCCCCATCCCCATCAGTCTTAATC
      |  AGTCTTGTTACGTTATGACT-AATCTTTGGGGATTGTGCAGAATGTTATTTTAGATAAGC
      |  AAAA-CGAGCAAAAT-GGGGAGTT-A-CTT-A-TATTT-CTTT-AAA--GC
      |  #G023uabh-(426)
      |  GTAACGT-ATGA-TCAATCTTTGGGGATTGTGCAGAATGT-ATTTTAGATAAGCAAAAAC
      |  GAGCAAAATAGGGGAGTTTAACTTTAATATTTTCTTTTAAAAAGCATTTCATGTTATAAG
      |  ATCAATTCTGAGTGGTAGAAATGCTTTGACATTTTATTTCCATTTTCTACTTTTAGTTTT
      |  TTTCCTATTTGTTTAAGATCGTAGAGGATTATTAAGCTGAACTCCTCAACTGATAAAAAG
      |  CATGACATCTTAAACATAAGCAAAGCATATTTTTAGGTTAATTTTCACATAGAAAACAGT
      |  TTATTTTATGTGAAATTCTATGTAGATATACTATTTTTTTGGTATTTATT
      |  #G006uaah-(496)
      |  GGGGAGTTTAACTTTAATATTTTCTTTTAAAAAGCATTTCATGTTATAAGATCAATTCTG
      |  AGTGGTAGAAATGCTTTGACATTTTATTTCCATTTTCTACTTTTAGTTTTTTTCCTATTT
      |  GTTTAAGATCTTAGAGGATTATTAAGCTGAACTCCTCAACTGATAAAAAGCATGACATCT
      |  TAAACATAAGCAAAGCATATNNT-AGGTTAATTTTCACATAGAAAACAGTTTATTTTATG
      |  T



   Slight modifications by S. Smith on Mon Feb 17 10:18:34 EST 1992.
   These changes allow for command line arguments for several
   of the hard coded parameters, as well as a slight modification to
   the output routine to support GDE format.  Changes are commented
   as: Mod by S.S.