
                                   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 17-1
8
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, basa
l
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        6
0
     aacctgagcg ggactggnag aaggagcaga gggaggcagc acccggcgtg acggnagtgt       12
0
     gtggggcact caggccttcc gcagtgtcat ctgccacacg gaaggcacgg ccacgggcag       18
0
     gggggtctat gatcttctgc atgcccagct ggcatggccc cacgtagagt ggnntggcgt       24
0
     ctcggtgctg gtcagcgaca cgttgtcctg gctgggcagg tccagctccc ggaggacctg       30
0
     gggcttcagc ttcccgtagc gctggctgca gtgacggatg ctcttgcgct gccatttctg       36
0
     ggtgctgtca ctgtccttgc tcactccaaa ccagttcggc ggtccccctg cggatggtct       42
0
     gtgttgatgg acgtttgggc tttgcagcac cggccgccga gttcatggtn gggtnaagag       48
0
     atttgggttt tttcn                                                        49
5
//

  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 shor
t
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     3084
0
     tctcctgggg ttcccacctc cacaaaaacc cccactgcta ggagtgcagg caggagggga     3090
0
     cctgagaacc gacagttata ggtcctgcgg gtgggcagtg ctgggtgttc tggtctgccc     3096
0
     cacccctgtg tgcctagatc cccatctggg cctcaagtgg gtgggattcc aaaggaagag     3102
0
     ccggagtagg cgtggggagg ggcaggccca ggctggacaa agagtctggc cagggagcgg     3108
0
     cacattgccc tcccagagac agtggctcag tgtccaggcc ttccccaggc gcacagtggg     3114
0
     ctcttgttcc cagaaagccc ctcgggggga tccaaacagt gtctccccca ccccgctgac     3120
0
     ccctcagtgt atggggaaac cgtggcccac ggaaggcctc actgcctggg gtcacacagc     3126
0
     atctgagtca ctgcagcagc ctcacagctg ccagcccagg cccagcccca tcaggagaca     3132
0
     cccaaagcca cagtgcatcc caggaccagc tgggggggct gcgggcagga ctctcgatga     3138
0
     ggctgaggga cgaggagggt caagggagcc actggcgcca tgcatgctga cgtcccctct     3144
0
     ggctgcctgc agagcctggt gtggaagggc tgagtggggg atggtggaga gtcctgttaa     3150
0
     ctcaggtttc tgctctgggg atgtctgggc acccatcaag ctggccgcgt gcacaggtgc     3156
0
     agggagagcc agaaagcagg agccgatgca gggaggccac tggggacagc ccaggctgat     3162
0
     gcttgggccc catgtgtctc caccacctac aaccctaagc aagcctcagc tttcccatct     3168
0
     ggaaatcagg ggtcacagca gtgcctggca cagtagcagc ggctgactcc atcacagggt     3174
0
     ggtgtagcct gtgggtactt ggcactctct gaggggcagg agctgggggg tgaaaggacc     3180
0
     ctagagcata tgcaacaaga gggcagccct ggggacacct ggggacagaa ccctccaaag     3186
0
     gtgtcgagtt tgggaagaga ctagagagaa gctctggcca gtccaggcat agacagtggc     3192
0
     cacagccagt ggagagctgc atcctcaggt gtgagcagca accacctctg tactcaggcc     3198
0
     tgccctgcac actcacagga ccatgctggc agggacaact ggcggcggag ttgactgcca     3204
0
     accccggggc cagaaccatc aagcctgggc tctgctccgc ccaaggaact gcctgctgcc     3210
0
     gaggtcagct ggagcaaggg gcctcacccc gggacacctt cccagacgtg tcctcagctc     3216
0
     acatgagcct catcccaggg ggatgtggct cctccagcat ccccacccac acgctgctct     3222
0
     ctgaccctca gtcttctgtt tgactcctaa tctgaagctc aatcctagat ctcccttgag     3228
0
     aagggggtca ccagctgtct ggcagcccag cctccaggtc ttctggatta atgaagggaa     3234
0
     agtcacctgg cctctctgcc ttgtctatta atggcatcat gctgagaatg atatttgcta     3240
0
     ggccctttgc aaaccccaaa gtgctcttca accctcccag tgaagcctct tcttttctgt     3246
0
     ggaagaaatg aggttcaggg tggagcaggg caggcctgag acctttgcag ggttctctcc     3252
0
     aggtccccag caggacagac tggcaccctg cctcccctca tcaccctaga caaggagaca     3258
0
     gaacaagagg ttccctgcta caggccatct gtgagggaag ccgccctagg gcctgtagac     3264
0
     acaggaatcc ctgaggacct gacctgtgag ggtagtgcac aaaggggcca gcacttggca     3270
0
     ggaggggggg gggcactgcc ccaaggctca gctagcaaat gtggcacagg ggtcaccaga     3276
0
     gctaaacccc tgactcagtt gggtctgaca ggggctgaca tggcagacac acccaggaat     3282
0
     caggggacac caagtgcagc tcagggcacc tgtccaggcc acacagtcag aaaggggatg     3288
0
     gcagcaagga cttagctaca ctagattctg ggggtaaact gcctggtatg ctggtcactg     3294
0
     ctagtcccca gtctggagtc tagctgggtc tcaggagtta ggcgaaaaca ccctccccag     3300
0
     gctgcaggtg ggagaggccc acatcccctg cacacgtctg gccagaggac agatgggcag     3306
0
     cccagtcacc agtcagagcc ctccagaggt gtccctgact gaccctacac acatgcaccc     3312
0
     aggtgcccag gcacccttgg gctcagcaac cctgcaaccc cctcccagga cccaccagaa     3318
0
     gcaggatagg actagagagg ccacaggagg gaaaccaagt cagagcagaa atggcttcgg     3324
0
     tcctcagcag cctggctcag cttcctcaaa ccagatcctg actgatcaca ctggtctgtc     3330
0
     taacccctgg gaggggtcct ctgtatccat cttacagata aggaaactga ggctcagaga     3336
0
     agcccatcac tgcctaaggt cccagggcct ataagggagc tcaaagcctt gggccaggtc     3342
0
     tgcccaggag ctgcagtgga agggaccctg tctgcagacc cccagaagac aaggcagacc     3348
0
     acctgggttc ttcagccttg tggctgtgga cggctgtcag acccttctaa gaccccttgc     3354
0
     cacctgctcc atcaggggca tctcagttga agaaggaagg actcaccccc aaaatcgtcc     3360
0
     aactcagaaa aaaaggcaga agccaaggaa tccaatcact gggcaaaatg tgatcctggc     3366
0
     acagacactg aggtggggga actggagccg gtgtggcgga ggccctcaca gccaagagca     3372
0
     actgggggtg ccctgggcag ggactgtagc tgggaagatc                           3376
0
//

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.
