                                    esim4



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Align an mRNA to a genomic DNA sequence

Description

   The original sim4 program was developed by Florea et al. for aligning
   cdna/est sequence to genomic sequences.

   The program is available for download from http://globin.cse.psu.edu/

Algorithm

   Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W. "A computer program
   for aligning a cDNA sequence with a genomic DNA sequence." Genome Res
   1998 Sep;8(9):967-74

Usage

   Here is a sample session with esim4


% esim4
Align an mRNA to a genomic DNA sequence
Input nucleotide sequence: tembl:h45989
Genomic sequence: tembl:z69719
Sim4 program output file [h45989.esim4]:


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

Command line arguments

Align an mRNA to a genomic DNA sequence
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-asequence]         sequence   Nucleotide sequence filename and optional
                                  format, or reference (input USA)
  [-bsequence]         seqall     Genomic sequence
  [-outfile]           outfile    [*.esim4] Sim4 program output file

   Additional (Optional) qualifiers (* if not always prompted):
   -word               integer    [12] Sets the word size (W) for blast hits.
                                  Default value: 12. (Any integer value)
   -extend             integer    [12] Sets the word extension termination
                                  limit (X) for the blast-like stage of the
                                  algorithm. Default value: 12. (Any integer
                                  value)
   -cutoff             integer    [3] Sets the cutoff (E) in range [3,10].
                                  (Integer up to 10)
   -useramsp           toggle     [N] False: esim4 calculates mspA, True:
                                  value from mspA command line argument.
*  -amsp               integer    [16] 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)
   -userbmsp           toggle     [N] False: esim4 calculates mspB, True:
                                  value from mspB command line argument.
*  -bmsp               integer    [12] 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)
   -weight             integer    [0] Weight value (H) (undocumented). 0 uses
                                  a default, >0 is a value (Any integer value)
   -diagonal           integer    [10] Bound (K) for the diagonal distance
                                  within consecutive MSPs in an exon. (Any
                                  integer value)
   -strand             menu       [both] 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'. (Values: both (Both
                                  strands); forward (Forward strand only);
                                  reverse (Reverse strand only))
   -format             integer    [0] 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)
   -cliptails          boolean    [N] 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    [N] 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    [Y] 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. (Any string)
   -aoffset            integer    [0] Undocumented (f) - some sort of offset
                                  in first sequence. (Any integer value)
   -boffset            integer    [0] Undocumented (F) - some sort of offset
                                  in second sequence. (Any integer value)
   -toa                integer    [0] Undocumented (t)- offset end of first
                                  sequence? (Any integer value)
   -tob                integer    [0] Undocumented (T) - offset end of second
                                  sequence? (Any integer value)

   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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit


Input file format

   esim4 reads any normal sequence USAs.

  Input files for usage example

   'tembl:h45989' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:h45989

ID   H45989; SV 1; linear; mRNA; EST; HUM; 495 BP.
XX
AC   H45989;
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; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   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   GDB; 3839990.
DR   GDB; 4193257.
DR   ImaGenes; ENSEp780A0214D.
DR   ImaGenes; ENSEp780A044Q.
DR   ImaGenes; HU3_p972A0639D.
DR   ImaGenes; HU3_p972B1110Q.
DR   ImaGenes; HU3_p983A0639D.
DR   ImaGenes; HU4_p940A0622D.
DR   ImaGenes; IMAGp956A0431Q.
DR   ImaGenes; IMAGp998F03326Q.
DR   ImaGenes; RZPDp1096A101D.
DR   ImaGenes; RZPDp1096A191Q.
DR   ImaGenes; RZPDp200A0214D.
DR   UNILIB; 555; 300.
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                   /organism="Homo sapiens"
FT                   /lab_host="DH10B (ampicillin resistant)"
FT                   /mol_type="mRNA"
FT                   /sex="Male"
FT                   /dev_stage="55-year old"
FT                   /clone_lib="Soares adult brain N2b5HB55Y"
FT                   /clone="IMAGE:177794"
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                   /db_xref="taxon:9606"
FT                   /db_xref="UNILIB:555"
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:z69719

ID   Z69719; SV 1; linear; genomic DNA; STD; HUM; 33760 BP.
XX
AC   Z69719;
XX
DT   26-FEB-1996 (Rel. 46, Created)
DT   13-JAN-2009 (Rel. 99, Last updated, Version 7)
XX
DE   Human DNA sequence from clone XX-CNFG9 on chromosome 16
XX
KW   C16orf33; HTG; POLR3K; RHBDF1.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-33760
RA   Kershaw J.;
RT   ;
RL   Submitted (09-JAN-2009) to the EMBL/GenBank/DDBJ databases.
RL   Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.
RL   E-mail enquiries: vega@sanger.ac.uk Clone requests: Geneservice
RL   (http://www.geneservice.co.uk/) and BACPAC Resources
RL   (http://bacpac.chori.org/)
XX
DR   EMBL-CON; GL000124.
DR   EMBL-JOIN; Z69720.
DR   GDB; 11502921.
XX
CC   -------------- Genome Center
CC   Center: Wellcome Trust Sanger Institute
CC   Center code: SC
CC   Web site: http://www.sanger.ac.uk
CC   Contact: vega@sanger.ac.uk
CC   --------------
CC
CC   This sequence was finished as follows unless otherwise noted: all regions
CC   were either double-stranded or sequenced with an alternate chemistry or
CC   covered by high quality data (i.e., phred quality >= 30); an attempt was
CC   made to resolve all sequencing problems, such as compressions and repeats;
CC   all regions were covered by at least one subclone; and the assembly was
CC   confirmed by restriction digest, except on the rare occasion of the clone
CC   being a YAC.
CC
CC   The following abbreviations are used to associate primary accession
CC   numbers given in the feature table with their source databases:
CC   Em:, EMBL; Sw:, SWISSPROT; Tr:, TREMBL; Wp:, WORMPEP;
CC   Information on the WORMPEP database can be found at
CC   http://www.sanger.ac.uk/Projects/C_elegans/wormpep


  [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: h45989.esim4


seq1 = H45989, 495 bp
seq2 = Z69719 (Z69719), 33760 bp

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

Data files

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
                    est2genome   Align EST sequences to genomic DNA sequence
                    needle       Needleman-Wunsch global alignment of two sequences
                    needleall    Many-to-many pairwise alignments of two sequence sets
                    stretcher    Needleman-Wunsch rapid global alignment of two sequences

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.
