
                                   esim4 



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

   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)
   -usermspa           toggle     [N] False: esim4 calculates mspA, True:
                                  value from mspA command line argument.
*  -mspa               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)
   -usermspb           toggle     [N] False: esim4 calculates mspB, True:
                                  value from mspB command line argument.
*  -mspb               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 is accepted)
   -offseta            integer    [0] Undocumented (f) - some sort of offset
                                  in first sequence. (Any integer value)
   -offsetb            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 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

   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   RZPD; IMAGp998F03326.
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 17-1
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                   /db_xref="taxon:9606"
FT                   /db_xref="RZPD:IMAGp998F03326"
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        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:z69719

ID   Z69719; SV 1; linear; genomic DNA; STD; HUM; 33760 BP.
XX
AC   Z69719;
XX
DT   26-FEB-1996 (Rel. 46, Created)
DT   18-JAN-2007 (Rel. 90, Last updated, Version 6)
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 (16-JAN-2007) 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:
RL   clonerequest@sanger.ac.uk
XX
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
XX
FH   Key             Location/Qualifiers


  [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: 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 and genomic DNA sequences
   needle       Needleman-Wunsch global alignment
   stretcher    Finds the best global alignment between 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.
