merger.txt

emboss的linux版本的源代码

                                  merger 



Function

   Merge two overlapping sequences

Description

   This joins two overlapping nucleic acid sequences into one merged
   sequence.

   It uses a global alignment algorithm (Needleman & Wunsch) to optimally
   align the sequences and then it creates the merged sequence from the
   alignment. When there is a mismatch in the alignment between the two
   sequences, the correct base to include in the resulting sequence is
   chosen by using the base from the sequence which has the best local
   sequence quality score. The following heuristic is used to find the
   sequence quality score:

   If one of the bases is a 'N', then the other sequence's base is used,
   else:

   A window size around the disputed base is used to find the local
   quality score. This window size is increased from 5, to 10 to 20 bases
   or until there is a clear decision on the best choice. If there is no
   best choice after using a window of 20, then the base in the first
   sequence is used.

   To calculate the quality of a window of a sequence around a base:
     * quality = sequence value/length under window either side of the
       base
     * sequence value = sum of points in that window
     * unambiguous bases (ACGTU) score 2 points
     * ambiguous bases (MRWSYKVHDB) score 1 point
     * Ns score 0 points
     * off end of the sequence scores 0 points

   N.B. This heavily discriminates against the iffy bits at the end of
   sequence reads.

   This program was originally written to aid in the reconstruction of
   mRNA sequences which had been sequenced from both ends as a 5' and 3'
   EST (cDNA). eg. joining two reads produced by primer walking
   sequencing.

   Care should be taken to reverse one of the sequences (e.g. using the
   qualifier '-sreverse2') if this is required to get them both in the
   correct orientation.

   Because it uses a Needleman & Wunsch alignment the required memory may
   be greater than the available memory when attempting to merge large
   (cosmid-sized or greater) sequences.

   The gap open and gap extension penalties have been set at a higher
   level than is usual (50 and 5). This was experimentally determined to
   give the best results with a set of poor quality EST test sequences.

Usage

   Here is a sample session with merger


% merger 
Merge two overlapping sequences
Input sequence: tembl:eclacy
Second sequence: tembl:eclaca
Output alignment [eclacy.merger]: 
output sequence [eclacy.fasta]: 

   Go to the input files for this example
   Go to the output files for this example

   Typically, one of the sequences will need to be reverse-complemented
   to put it into the correct orientation to make it join. For example:

% merger file1.seq file2.seq -sreverse2 -outseq merged.seq

Command line arguments

   Standard (Mandatory) qualifiers:
  [-asequence]         sequence   Sequence filename and optional format, or
                                  reference (input USA)
  [-bsequence]         sequence   Sequence filename and optional format, or
                                  reference (input USA)
  [-outfile]           align      [*.merger] Output alignment file name
  [-outseq]            seqout     [.] Sequence filename and
                                  optional format (output USA)

   Additional (Optional) qualifiers:
   -datafile           matrixf    [EBLOSUM62 for protein, EDNAFULL for DNA]
                                  This is the scoring matrix file used when
                                  comparing sequences. By default it is the
                                  file 'EBLOSUM62' (for proteins) or the file
                                  'EDNAFULL' (for nucleic sequences). These
                                  files are found in the 'data' directory of
                                  the EMBOSS installation.
   -gapopen            float      [@($(acdprotein)? 50.0 : 50.0 )] Gap opening
                                  penalty (Number from 0.000 to 100.000)
   -gapextend          float      [@($(acdprotein)? 5.0 : 5.0)] Gap extension
                                  penalty (Number from 0.000 to 10.000)

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-asequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-bsequence" associated qualifiers
   -sbegin2            integer    Start of the sequence to be used
   -send2              integer    End of the sequence to be used
   -sreverse2          boolean    Reverse (if DNA)
   -sask2              boolean    Ask for begin/end/reverse
   -snucleotide2       boolean    Sequence is nucleotide
   -sprotein2          boolean    Sequence is protein
   -slower2            boolean    Make lower case
   -supper2            boolean    Make upper case
   -sformat2           string     Input sequence format
   -sdbname2           string     Database name
   -sid2               string     Entryname
   -ufo2               string     UFO features
   -fformat2           string     Features format
   -fopenfile2         string     Features file name

   "-outfile" associated qualifiers
   -aformat3           string     Alignment format
   -aextension3        string     File name extension
   -adirectory3        string     Output directory
   -aname3             string     Base file name
   -awidth3            integer    Alignment width
   -aaccshow3          boolean    Show accession number in the header
   -adesshow3          boolean    Show description in the header
   -ausashow3          boolean    Show the full USA in the alignment
   -aglobal3           boolean    Show the full sequence in alignment

   "-outseq" associated qualifiers
   -osformat4          string     Output seq format
   -osextension4       string     File name extension
   -osname4            string     Base file name
   -osdirectory4       string     Output directory
   -osdbname4          string     Database name to add
   -ossingle4          boolean    Separate file for each entry
   -oufo4              string     UFO features
   -offormat4          string     Features format
   -ofname4            string     Features file name
   -ofdirectory4       string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

   merger reads any two sequence USAs of the same type (protein or
   nucleic acid.)

  Input files for usage example

   'tembl:eclacy' is a sequence entry in the example nucleic acid
   database 'tembl'

  Database entry: tembl:eclacy

ID   ECLACY     standard; DNA; PRO; 1500 BP.
XX
AC   V00295;
XX
SV   V00295.1
XX
DT   09-JUN-1982 (Rel. 01, Created)
DT   07-JUL-1995 (Rel. 44, Last updated, Version 4)
XX
DE   E. coli lacY gene (codes for lactose permease).
XX
KW   membrane protein.
XX
OS   Escherichia coli
OC   Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
OC   Escherichia.
XX
RN   [1]
RP   1-1500
RX   MEDLINE; 80120651.
RA   Buechel D.E., Gronenborn B., Mueller-Hill B.;
RT   "Sequence of the lactose permease gene";
RL   Nature 283:541-545(1980).
XX
DR   SWISS-PROT; P00722; BGAL_ECOLI.
DR   SWISS-PROT; P02920; LACY_ECOLI.
DR   SWISS-PROT; P07464; THGA_ECOLI.
XX
CC   lacZ is a beta-galactosidase and lacA is transacetylase.
CC   KST ECO.LACY
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1500
FT                   /db_xref="taxon:562"
FT                   /organism="Escherichia coli"
FT   CDS             <1..54
FT                   /codon_start=1
FT                   /db_xref="SWISS-PROT:P00722"
FT                   /note="reading frame (lacZ)"
FT                   /transl_table=11
FT                   /protein_id="CAA23570.1"
FT                   /translation="FQLSAGRYHYQLVWCQK"
FT   CDS             106..1359
FT                   /db_xref="SWISS-PROT:P02920"
FT                   /note="reading frame (lacY)"
FT                   /transl_table=11
FT                   /protein_id="CAA23571.1"
FT                   /translation="MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSD
T
FT                   GIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNI
L
FT                   VGSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMF
T
FT                   INNQFVFWLGSGCALILAVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPK
L
FT                   WFLSLYVIGVSCTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAP
L
FT                   IINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITS
Q
FT                   FEVRFSATIYLVCFCFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVF
T
FT                   LSGPGPLSLLRRQVNEVA"
FT   CDS             1423..>1500
FT                   /db_xref="SWISS-PROT:P07464"
FT                   /note="reading frame (lacA)"
FT                   /transl_table=11
FT                   /protein_id="CAA23572.1"
FT                   /translation="MNMPMTERIRAGKLFTDMCEGLPEKR"
XX
SQ   Sequence 1500 BP; 315 A; 342 C; 357 G; 486 T; 0 other;
     ttccagctga gcgccggtcg ctaccattac cagttggtct ggtgtcaaaa ataataataa        6
0
     ccgggcaggc catgtctgcc cgtatttcgc gtaaggaaat ccattatgta ctatttaaaa       12
0
     aacacaaact tttggatgtt cggtttattc tttttctttt acttttttat catgggagcc       18
0
     tacttcccgt ttttcccgat ttggctacat gacatcaacc atatcagcaa aagtgatacg       24
0
     ggtattattt ttgccgctat ttctctgttc tcgctattat tccaaccgct gtttggtctg       30
0
     ctttctgaca aactcgggct gcgcaaatac ctgctgtgga ttattaccgg catgttagtg       36
0
     atgtttgcgc cgttctttat ttttatcttc gggccactgt tacaatacaa cattttagta       42
0
     ggatcgattg ttggtggtat ttatctaggc ttttgtttta acgccggtgc gccagcagta       48
0
     gaggcattta ttgagaaagt cagccgtcgc agtaatttcg aatttggtcg cgcgcggatg       54
0
     tttggctgtg ttggctgggc gctgtgtgcc tcgattgtcg gcatcatgtt caccatcaat       60
0
     aatcagtttg ttttctggct gggctctggc tgtgcactca tcctcgccgt tttactcttt       66
0
     ttcgccaaaa cggatgcgcc ctcttctgcc acggttgcca atgcggtagg tgccaaccat       72
0
     tcggcattta gccttaagct ggcactggaa ctgttcagac agccaaaact gtggtttttg       78
0
     tcactgtatg ttattggcgt ttcctgcacc tacgatgttt ttgaccaaca gtttgctaat       84
0
     ttctttactt cgttctttgc taccggtgaa cagggtacgc gggtatttgg ctacgtaacg       90
0
     acaatgggcg aattacttaa cgcctcgatt atgttctttg cgccactgat cattaatcgc       96
0
     atcggtggga aaaacgccct gctgctggct ggcactatta tgtctgtacg tattattggc      102
0
     tcatcgttcg ccacctcagc gctggaagtg gttattctga aaacgctgca tatgtttgaa      108
0
     gtaccgttcc tgctggtggg ctgctttaaa tatattacca gccagtttga agtgcgtttt      114
0
     tcagcgacga tttatctggt ctgtttctgc ttctttaagc aactggcgat gatttttatg      120
0
     tctgtactgg cgggcaatat gtatgaaagc atcggtttcc agggcgctta tctggtgctg      126
0
     ggtctggtgg cgctgggctt caccttaatt tccgtgttca cgcttagcgg ccccggcccg      132
0
     ctttccctgc tgcgtcgtca ggtgaatgaa gtcgcttaag caatcaatgt cggatgcggc      138
0
     gcgacgctta tccgaccaac atatcataac ggagtgatcg cattgaacat gccaatgacc      144
0
     gaaagaataa gagcaggcaa gctatttacc gatatgtgcg aaggcttacc ggaaaaaaga      150
0
//

  Database entry: tembl:eclaca

ID   ECLACA     standard; DNA; PRO; 1832 BP.
XX
AC   X51872;
XX
SV   X51872.1
XX
DT   17-APR-1990 (Rel. 23, Created)
DT   05-JUL-1999 (Rel. 60, Last updated, Version 5)
XX
DE   Escherichia coli lacA gene for thiogalactoside transacetylase
XX
KW   lac operon; lacA gene; lacY gene; thiogalactoside transacetylase.
XX
OS   Escherichia coli
OC   Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
OC   Escherichia.
XX
RN   [1]
RC   (1-1832)
RP   1-1832