| esim4

## Function

Align an mRNA to a genomic DNA sequence

## Description

**************** EDIT HERE ****************

## Algorithm

**************** EDIT HERE ****************

## Usage

Here is a sample session with esim4

    % esim4
    Align an mRNA to a genomic DNA sequence
    Input sequence: tembl:hs989235
    Genomic sequence: tembl:hsnfg9
    Output file [hs989235.esim4]:

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

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-asequence]         sequence   Sequence USA
      [-bsequence]         seqall     Genomic sequence
      [-outfile]           outfile    Output file name

       Additional (Optional) qualifiers (* if not always prompted):
       -word               integer    Sets the word size (W) for blast hits.
                                      Default value: 12.
       -extend             integer    Sets the word extension termination limit
                                      (X) for the blast-like stage of the
                                      algorithm. Default value: 12.
       -cutoff             integer    Sets the cutoff (E) in range [3,10].
       -usermspa           toggle     False: esim4 calculates mspA, True: value
                                      from mspA command line argument.
    *  -mspa               integer    MSP score threshold (K) for the first stage
                                      of the algorithm. (If this option is not
                                      specified, the threshold is computed from
                                      the lengths of the sequences, using
                                      statistical criteria.) For example, a good
                                      value for genomic sequences in the range of
                                      a few hundred Kb is 16. To avoid spurious
                                      matches, however, a larger value may be
                                      needed for longer sequences.
       -usermspb           toggle     False: esim4 calculates mspB, True: value
                                      from mspB command line argument.
    *  -mspb               integer    Sets the threshold for the MSP scores (C)
                                      when aligning the as-yet-unmatched
                                      fragments, during the second stage of the
                                      algorithm. By default, the smaller of the
                                      constant 12 and a statistics-based threshold
                                      is chosen.
       -weight             integer    Weight value (H) (undocumented). 0 uses a
                                      default, >0 is a value
       -diagonal           integer    Bound (K) for the diagonal distance within
                                      consecutive MSPs in an exon.
       -strand             menu       This determines the strand of the genome (R)
                                      with which the mRNA will be aligned. The
                                      default value is 'both', in which case both
                                      strands of the genome are attempted. The
                                      other allowed modes are 'forward' and
                                      'reverse'.
       -format             integer    Sets the output format (A). Exon endpoints
                                      only (format=0), exon endpoints and
                                      boundaries of the coding region (CDS) in the
                                      genomic sequence, when specified for the
                                      input mRNA (-format=5), alignment text
                                      (-format=1), alignment in lav-block format
                                      (-format=2), or both exon endpoints and
                                      alignment text (-format=3 or -format=4). If
                                      a reverse complement match is found,
                                      -format=0,1,2,3,5 will give its position in
                                      the plus strand of the longer sequence and
                                      the minus strand of the shorter sequence.
                                      -format=4 will give its position in the plus
                                      strand of the first sequence (mRNA) and the
                                      minus strand of the second sequence
                                      (genome), regardless of which sequence is
                                      longer. The -format=5 option can be used
                                      with the S command line option to specify
                                      the endpoints of the CDS in the mRNA, and
                                      produces output in the exons file format
                                      required by PipMaker.
       -cliptails          boolean    Trim poly-A tails (P). Specifies whether or
                                      not the program should report the fragment
                                      of the alignment containing the poly-A tail
                                      (if found). By default (-nocliptails) the
                                      alignment is displayed as computed. When
                                      this feature is enabled (-cliptails), sim4
                                      will remove the poly-A tails and all format
                                      options will produce additional lav
                                      alignment headers.
       -smallexons         boolean    Requests an additional search for small
                                      marginal exons (N) (N=1) guided by the
                                      splice-site recognition signals. This option
                                      can be used when a high accuracy match is
                                      expected. The default value is N=0,
                                      specifying no additional search.
       -[no]ambiguity      boolean    Controls the set of characters allowed in
                                      the input sequences (B). By default
                                      (-ambiguity), ambiguity characters
                                      (ABCDGHKMNRSTVWXY) are allowed. By
                                      specifying -noambiguity, the set of
                                      acceptable characters is restricted to
                                      A,C,G,T,N and X only.
       -cdsregion          string     Allows the user to specify the endpoints of
                                      the CDS in the input mRNA (S), with the
                                      syntax: -cdsregion=n1..n2. This option is
                                      only available with the -format=5 flag,
                                      which produces output in the format required
                                      by PipMaker. Alternatively, the CDS
                                      coordinates could appear in a construct
                                      CDS=n1..n2 in the FastA header of the mRNA
                                      sequence. When the second file is an mRNA
                                      database, the command line specification for
                                      the CDS will apply to the first sequence in
                                      the file only.
       -offseta            integer    Undocumented (f) - some sort of offset in
                                      first sequence.
       -offsetb            integer    Undocumented (F) - some sort of offset in
                                      second sequence.
       -toa                integer    Undocumented (t)- offset end of first
                                      sequence?
       -tob                integer    Undocumented (T) - offset end of second
                                      sequence?

       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 each sequence to be used
       -send2              integer    End of each 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
       -odirectory3        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 deaths

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-asequence] (Parameter 1) | Sequence USA | Readable sequence | Required
[-bsequence] (Parameter 2) | Genomic sequence | Readable sequence(s) | Required
[-outfile] (Parameter 3) | Output file name | Output file | <sequence>.esim4
Additional (Optional) qualifiers | Allowed values | Default
-word | Sets the word size (W) for blast hits. Default value: 12. | Any integer value | 12
-extend | Sets the word extension termination limit (X) for the blast-like stage of the algorithm. Default value: 12. | Any integer value | 12
-cutoff | Sets the cutoff (E) in range [3,10]. | Integer up to 10 | 3
-usermspa | False: esim4 calculates mspA, True: value from mspA command line argument. | Toggle value Yes/No | No
-mspa | MSP score threshold (K) for the first stage of the algorithm. (If this option is not specified, the threshold is computed from the lengths of the sequences, using statistical criteria.) For example, a good value for genomic sequences in the range of a few hundred Kb is 16. To avoid spurious matches, however, a larger value may be needed for longer sequences. | Any integer value | 16
-usermspb | False: esim4 calculates mspB, True: value from mspB command line argument. | Toggle value Yes/No | No
-mspb | Sets the threshold for the MSP scores (C) when aligning the as-yet-unmatched fragments, during the second stage of the algorithm. By default, the smaller of the constant 12 and a statistics-based threshold is chosen. | Any integer value | 12
-weight | Weight value (H) (undocumented). 0 uses a default, >0 is a value | Any integer value | 0
-diagonal | Bound (K) for the diagonal distance within consecutive MSPs in an exon. | Any integer value | 10
-strand | This determines the strand of the genome (R) with which the mRNA will be aligned. The default value is 'both', in which case both strands of the genome are attempted. The other allowed modes are 'forward' and 'reverse'. |
both | (Both strands)
forward | (Forward strand only)
reverse | (Reverse strand only)
| both
-format | Sets the output format (A). Exon endpoints only (format=0), exon endpoints and boundaries of the coding region (CDS) in the genomic sequence, when specified for the input mRNA (-format=5), alignment text (-format=1), alignment in lav-block format (-format=2), or both exon endpoints and alignment text (-format=3 or -format=4). If a reverse complement match is found, -format=0,1,2,3,5 will give its position in the plus strand of the longer sequence and the minus strand of the shorter sequence. -format=4 will give its position in the plus strand of the first sequence (mRNA) and the minus strand of the second sequence (genome), regardless of which sequence is longer. The -format=5 option can be used with the S command line option to specify the endpoints of the CDS in the mRNA, and produces output in the exons file format required by PipMaker. | Integer from 0 to 5 | 0
-cliptails | Trim poly-A tails (P). Specifies whether or not the program should report the fragment of the alignment containing the poly-A tail (if found). By default (-nocliptails) the alignment is displayed as computed. When this feature is enabled (-cliptails), sim4 will remove the poly-A tails and all format options will produce additional lav alignment headers. | Boolean value Yes/No | No
-smallexons | Requests an additional search for small marginal exons (N) (N=1) guided by the splice-site recognition signals. This option can be used when a high accuracy match is expected. The default value is N=0, specifying no additional search. | Boolean value Yes/No | No
-[no]ambiguity | Controls the set of characters allowed in the input sequences (B). By default (-ambiguity), ambiguity characters (ABCDGHKMNRSTVWXY) are allowed. By specifying -noambiguity, the set of acceptable characters is restricted to A,C,G,T,N and X only. | Boolean value Yes/No | Yes
-cdsregion | Allows the user to specify the endpoints of the CDS in the input mRNA (S), with the syntax: -cdsregion=n1..n2. This option is only available with the -format=5 flag, which produces output in the format required by PipMaker. Alternatively, the CDS coordinates could appear in a construct CDS=n1..n2 in the FastA header of the mRNA sequence. When the second file is an mRNA database, the command line specification for the CDS will apply to the first sequence in the file only. | Any string is accepted | An empty string is accepted
-offseta | Undocumented (f) - some sort of offset in first sequence. | Any integer value | 0
-offsetb | Undocumented (F) - some sort of offset in second sequence. | Any integer value | 0
-toa | Undocumented (t)- offset end of first sequence? | Any integer value | 0
-tob | Undocumented (T) - offset end of second sequence? | Any integer value | 0
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

esim4 reads any normal sequence USAs.

### Input files for usage example

'tembl:hs989235' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:hs989235

    ID   HS989235   standard; RNA; EST; 495 BP.
    XX
    AC   H45989;
    XX
    SV   H45989.1
    XX
    DT   18-NOV-1995 (Rel. 45, Created)
    DT   04-MAR-2000 (Rel. 63, Last updated, Version 2)
    XX
    DE   yo13c02.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone
    DE   IMAGE:177794 3', mRNA sequence.
    XX
    KW   EST.
    XX
    OS   Homo sapiens (human)
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
    OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
    XX
    RN   [1]
    RP   1-495
    RA   Hillier L., Clark N., Dubuque T., Elliston K., Hawkins M., Holman M.,
    RA   Hultman M., Kucaba T., Le M., Lennon G., Marra M., Parsons J., Rifkin L.,
    RA   Rohlfing T., Soares M., Tan F., Trevaskis E., Waterston R., Williamson A.,
    RA   Wohldmann P., Wilson R.;
    RT   "The WashU-Merck EST Project";
    RL   Unpublished.
    XX
    DR   RZPD; IMAGp998F03326; IMAGp998F03326.
    XX
    CC   On May 8, 1995 this sequence version replaced gi:800819.
    CC   Contact: Wilson RK
    CC   Washington University School of Medicine
    CC   4444 Forest Park Parkway, Box 8501, St. Louis, MO 63108
    CC   Tel: 314 286 1800
    CC   Fax: 314 286 1810
    CC   Email: est@watson.wustl.edu
    CC   Insert Size: 544
    CC   High quality sequence stops: 265
    CC   Source: IMAGE Consortium, LLNL
    CC   This clone is available royalty-free through LLNL ; contact the
    CC   IMAGE Consortium (info@image.llnl.gov) for further information.
    CC   Possible reversed clone: polyT not found
    CC   Insert Length: 544   Std Error: 0.00
    CC   Seq primer: SP6
    CC   High quality sequence stop: 265.
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   source          1..495
    FT                   /db_xref="taxon:9606"
    FT                   /db_xref="ESTLIB:300"
    FT                   /db_xref="RZPD:IMAGp998F03326"
    FT                   /note="Organ: brain; Vector: pT7T3D (Pharmacia) with a
    FT                   modified polylinker; Site_1: Not I; Site_2: Eco RI; 1st
    FT                   strand cDNA was primed with a Not I - oligo(dT) primer [5'
    FT                   TGTTACCAATCTGAAGTGGGAGCGGCCGCGCTTTTTTTTTTTTTTTTTTT 3'],
    FT                   double-stranded cDNA was size selected, ligated to Eco RI
    FT                   adapters (Pharmacia), digested with Not I and cloned into
    FT                   the Not I and Eco RI sites of a modified pT7T3 vector
    FT                   (Pharmacia). Library went through one round of
    FT                   normalization to a Cot = 53. Library constructed by Bento
    FT                   Soares and M.Fatima Bonaldo. The adult brain RNA was
    FT                   provided by Dr. Donald H. Gilden. Tissue was acquired 17-18
    FT                   hours after death which occurred in consequence of a
    FT                   ruptured aortic aneurysm. RNA was prepared from a pool of
    FT                   tissues representing the following areas of the brain:
    FT                   frontal, parietal, temporal and occipital cortex from the
    FT                   left and right hemispheres, subcortical white matter, basal
    FT                   ganglia, thalamus, cerebellum, midbrain, pons and medulla."
    FT                   /sex="Male"
    FT                   /organism="Homo sapiens"
    FT                   /clone="IMAGE:177794"
    FT                   /clone_lib="Soares adult brain N2b5HB55Y"
    FT                   /dev_stage="55-year old"
    FT                   /lab_host="DH10B (ampicillin resistant)"
    XX
    SQ   Sequence 495 BP; 73 A; 135 C; 169 G; 104 T; 14 other;
         ccggnaagct cancttggac caccgactct cgantgnntc gccgcgggag ccggntggan        60
         aacctgagcg ggactggnag aaggagcaga gggaggcagc acccggcgtg acggnagtgt       120
         gtggggcact caggccttcc gcagtgtcat ctgccacacg gaaggcacgg ccacgggcag       180
         gggggtctat gatcttctgc atgcccagct ggcatggccc cacgtagagt ggnntggcgt       240
         ctcggtgctg gtcagcgaca cgttgtcctg gctgggcagg tccagctccc ggaggacctg       300
         gggcttcagc ttcccgtagc gctggctgca gtgacggatg ctcttgcgct gccatttctg       360
         ggtgctgtca ctgtccttgc tcactccaaa ccagttcggc ggtccccctg cggatggtct       420
         gtgttgatgg acgtttgggc tttgcagcac cggccgccga gttcatggtn gggtnaagag       480
         atttgggttt tttcn                                                        495
    //

### Database entry: tembl:hsnfg9

    ID   HSNFG9     standard; DNA; HUM; 33760 BP.
    XX
    AC   Z69719;
    XX
    SV   Z69719.1
    XX
    DT   26-FEB-1996 (Rel. 46, Created)
    DT   22-NOV-1999 (Rel. 61, Last updated, Version 3)
    XX
    DE   Human DNA sequence from cosmid NFG9 from a contig from the tip of the short
    DE   arm of chromosome 16, spanning 2Mb of 16p13.3. Contains Interleukin 9
    DE   Receptor Pseudogene, repeat polymorphism, ESTs, CpG islands and endogenous
    DE   retroviral DNA.
    XX
    KW   16p13.3; CpG island; Interleukin 9 Receptor Pseudogene;
    KW   repeat polymorphism.
    XX
    OS   Homo sapiens (human)
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
    OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
    XX
    RN   [1]
    RP   1-33760
    RA   Kershaw J.;
    RT   ;
    RL   Submitted (22-FEB-1996) to the EMBL/GenBank/DDBJ databases.
    RL   Sanger Centre, Hinxton, Cambridgeshire, CB10 1RQ, England. E-mail enquires:
    RL   humquery@sanger.ac.uk
    XX
    CC   IMPORTANT:  This sequence is not the entire insert of clone
    CC   NFG9.  It may be shorter because we only sequence overlapping
    CC   sections once, or longer because we arrange for a small
    CC   overlap between neighbouring submissions.
    XX
    CC   The true left end of clone NFG9 is at 1 in this sequence.
    CC   The true left end of clone RA36 is at 25872.
    XX
    CC   NFG9 is from a 280kb clone contig extending from the telomere of 16p.
    CC   Higgs D.R., Flint J. unpublished. MRC Molecular Haematology Unit,
    CC   Institute of Molecular Medicine, Oxford.
    CC   NFG9 is from the library CV007K. Choo et al.,(1986) Gene 46. 277-286.
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   source          1..33760
    FT                   /chromosome="16"
    FT                   /db_xref="taxon:9606"
    FT                   /organism="Homo sapiens"
    FT                   /map="16p13.3"
    FT                   /clone_lib="CV007K"

      [Part of this file has been deleted for brevity]

         gagacagcag agtgctcagc tcatgaagga ggcaccagcc gccatgcctc tacatccagg     30840
         tctcctgggg ttcccacctc cacaaaaacc cccactgcta ggagtgcagg caggagggga     30900
         cctgagaacc gacagttata ggtcctgcgg gtgggcagtg ctgggtgttc tggtctgccc     30960
         cacccctgtg tgcctagatc cccatctggg cctcaagtgg gtgggattcc aaaggaagag     31020
         ccggagtagg cgtggggagg ggcaggccca ggctggacaa agagtctggc cagggagcgg     31080
         cacattgccc tcccagagac agtggctcag tgtccaggcc ttccccaggc gcacagtggg     31140
         ctcttgttcc cagaaagccc ctcgggggga tccaaacagt gtctccccca ccccgctgac     31200
         ccctcagtgt atggggaaac cgtggcccac ggaaggcctc actgcctggg gtcacacagc     31260
         atctgagtca ctgcagcagc ctcacagctg ccagcccagg cccagcccca tcaggagaca     31320
         cccaaagcca cagtgcatcc caggaccagc tgggggggct gcgggcagga ctctcgatga     31380
         ggctgaggga cgaggagggt caagggagcc actggcgcca tgcatgctga cgtcccctct     31440
         ggctgcctgc agagcctggt gtggaagggc tgagtggggg atggtggaga gtcctgttaa     31500
         ctcaggtttc tgctctgggg atgtctgggc acccatcaag ctggccgcgt gcacaggtgc     31560
         agggagagcc agaaagcagg agccgatgca gggaggccac tggggacagc ccaggctgat     31620
         gcttgggccc catgtgtctc caccacctac aaccctaagc aagcctcagc tttcccatct     31680
         ggaaatcagg ggtcacagca gtgcctggca cagtagcagc ggctgactcc atcacagggt     31740
         ggtgtagcct gtgggtactt ggcactctct gaggggcagg agctgggggg tgaaaggacc     31800
         ctagagcata tgcaacaaga gggcagccct ggggacacct ggggacagaa ccctccaaag     31860
         gtgtcgagtt tgggaagaga ctagagagaa gctctggcca gtccaggcat agacagtggc     31920
         cacagccagt ggagagctgc atcctcaggt gtgagcagca accacctctg tactcaggcc     31980
         tgccctgcac actcacagga ccatgctggc agggacaact ggcggcggag ttgactgcca     32040
         accccggggc cagaaccatc aagcctgggc tctgctccgc ccaaggaact gcctgctgcc     32100
         gaggtcagct ggagcaaggg gcctcacccc gggacacctt cccagacgtg tcctcagctc     32160
         acatgagcct catcccaggg ggatgtggct cctccagcat ccccacccac acgctgctct     32220
         ctgaccctca gtcttctgtt tgactcctaa tctgaagctc aatcctagat ctcccttgag     32280
         aagggggtca ccagctgtct ggcagcccag cctccaggtc ttctggatta atgaagggaa     32340
         agtcacctgg cctctctgcc ttgtctatta atggcatcat gctgagaatg atatttgcta     32400
         ggccctttgc aaaccccaaa gtgctcttca accctcccag tgaagcctct tcttttctgt     32460
         ggaagaaatg aggttcaggg tggagcaggg caggcctgag acctttgcag ggttctctcc     32520
         aggtccccag caggacagac tggcaccctg cctcccctca tcaccctaga caaggagaca     32580
         gaacaagagg ttccctgcta caggccatct gtgagggaag ccgccctagg gcctgtagac     32640
         acaggaatcc ctgaggacct gacctgtgag ggtagtgcac aaaggggcca gcacttggca     32700
         ggaggggggg gggcactgcc ccaaggctca gctagcaaat gtggcacagg ggtcaccaga     32760
         gctaaacccc tgactcagtt gggtctgaca ggggctgaca tggcagacac acccaggaat     32820
         caggggacac caagtgcagc tcagggcacc tgtccaggcc acacagtcag aaaggggatg     32880
         gcagcaagga cttagctaca ctagattctg ggggtaaact gcctggtatg ctggtcactg     32940
         ctagtcccca gtctggagtc tagctgggtc tcaggagtta ggcgaaaaca ccctccccag     33000
         gctgcaggtg ggagaggccc acatcccctg cacacgtctg gccagaggac agatgggcag     33060
         cccagtcacc agtcagagcc ctccagaggt gtccctgact gaccctacac acatgcaccc     33120
         aggtgcccag gcacccttgg gctcagcaac cctgcaaccc cctcccagga cccaccagaa     33180
         gcaggatagg actagagagg ccacaggagg gaaaccaagt cagagcagaa atggcttcgg     33240
         tcctcagcag cctggctcag cttcctcaaa ccagatcctg actgatcaca ctggtctgtc     33300
         taacccctgg gaggggtcct ctgtatccat cttacagata aggaaactga ggctcagaga     33360
         agcccatcac tgcctaaggt cccagggcct ataagggagc tcaaagcctt gggccaggtc     33420
         tgcccaggag ctgcagtgga agggaccctg tctgcagacc cccagaagac aaggcagacc     33480
         acctgggttc ttcagccttg tggctgtgga cggctgtcag acccttctaa gaccccttgc     33540
         cacctgctcc atcaggggca tctcagttga agaaggaagg actcaccccc aaaatcgtcc     33600
         aactcagaaa aaaaggcaga agccaaggaa tccaatcact gggcaaaatg tgatcctggc     33660
         acagacactg aggtggggga actggagccg gtgtggcgga ggccctcaca gccaagagca     33720
         actgggggtg ccctgggcag ggactgtagc tgggaagatc                           33760
    //

## Output file format

esim4 outputs a graph to the specified graphics device. outputs a report format file. The default format is ...

### Output files for usage example

### File: hs989235.esim4

    seq1 = HS989235, 495 bp
    seq2 = HSNFG9 (HSNFG9), 33760 bp

    1-193  (25686-25874)   92% <-
    194-407  (26279-26492)   98% <-
    408-487  (27391-27469)   88%

## Data files

**************** EDIT HERE ****************

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
alignrunner | Runs alignment program on all sequence pairs in a directory
contactalign | EMBOSS implementation of Damian Counsell's 2.5-D alignment algorithm
est2genome | Align EST and genomic DNA sequences
nawalign | Damian Counsell's implementation for protein sequences of the Needleman and Wunsch alignment algorithm
nawalignrunner | Runs nawalign alignment program on all sequence pairs in a directory
needle | Needleman-Wunsch global alignment
needlerunner | Runs needle alignment program on all sequence pairs in a directory
scorer | Scores accuracy of protein-protein sequence alignment against gold standard structure-structure alignment
scorerrunner | Runs scorer to compare ordered pairs of substituted seqs in two directories and write the scores to a third
stretcher | Finds the best global alignment between two sequences
substitute | Substitutes matches from first (query) sequence of two aligned sequences in a trace into second (template sequence)
substituterunner | Runs substitute on directory of traces and writes substituted sequences to another

## Author(s)

This program is an EMBOSS conversion of a program written by Liliana Florea as part of the SIM4 package.

Although we take every care to ensure that the results of the EMBOSS version are identical to those from the original package, we recommend that you check your inputs give the same results in both versions before publication.

Please report all bugs in the EMBOSS version to the EMBOSS bug team, not to the original author.

## History

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.