Bio::Tools::Blast::Run::Webblast(3)

NAME
Bio::Tools::Blast::Run::Webblast.pm - Bioperl module for running Blast analyses using a HTTP interface.

SYNOPSIS
    # Run a Blast
    use Bio::Tools::Blast::Run::Webblast qw(&blast_remote);
    @out_file_names = &blast_remote($object, %named_parameters);
the blast_remote manpage is the only exported method of this module and it returns a list of local file names containing the Blast reports. "$object" is a reference to a Bio::Root::Object.pm object or subclass. See the blast_remote manpage() for a description of available parameters.

    # Obtain a list of available databases
    use Bio::Tools::Blast::Run::Webblast qw(@Blast_dbp_remote
                                            @Blast_dbn_remote);
    @amino_dbs      = @Blast_dbp_remote;
    @nucleotide_dbs = @Blast_dbn_remote;

INSTALLATION
This module is included with the central Bioperl distribution:

   http://bio.perl.org/Core/Latest
   ftp://bio.perl.org/pub/DIST
Follow the installation instructions included in the README file.

DESCRIPTION
Bio::Tools::Blast::Run::Webblast.pm contains methods and data necessary for running Blast sequence analyses using a remote server and saving the results locally.

Bio::Tools::Blast::run() provides an interface for Webblast.pm, so, ideally, you shouldn't use Webblast.pm directly, but via Blast.pm.

FEATURES:

• Supports NCBI Blast1, Blast2, and PSI-Blast servers as well as WashU-Blast servers.
• Can operate through a proxy server enabling operation from behind a firewall.
• Can save reports with and without HTML formatting.
• Uses LWP.

In principle, this module can be customized to use different servers that provide a Blast interface like the NCBI or WashU style servers. Such servers could be remote or local. This hasn't been well-tested however.

DEPENDENCIES
Bio::Tools::Blast::Run::Webblast.pm is used by Bio::Tools::Blast.pm. The development of this is thus linked with the Blast.pm module.

SEE ALSO
 Bio::Tools::Blast.pm                    - Blast object.
 Bio::Tools::Blast::Run::LocalBlast.pm   - Utility module for running Blasts locally.
 Bio::Tools::Blast::HTML.pm              - Blast HTML-formating utility class.
 Bio::Seq.pm                             - Biosequence object
 Bio::Root::Object.pm                    - Bioperl base object class.
 http://bio.perl.org/Projects/modules.html  - Online module documentation
 http://bio.perl.org/Projects/Blast/        - Bioperl Blast Project
 http://bio.perl.org/                       - Bioperl Project Homepage

FEEDBACK

  Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                 - General discussion
  http://bio.perl.org/MailList.html  - About the mailing lists

  Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bioperl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR

Steve A. Chervitz <sac@genome.stanford.edu>
        - Webblast.pm modularized version of webblast script.

Alex Dong Li <ali@genet.sickkids.on.ca>
        - original webblast script.

Ross N. Crowhurst <RCrowhurst@hort.cri.nz>
        - modified Webblast.pm to use LWP to give proxy server support.

VERSION
Bio::Tools::Blast::Run::Webblast.pm, 1.24

COPYRIGHT
Copyright (c) 1998, 1999 Steve A. Chervitz, Alex Dong Li, Ross N. Crowhurst. All Rights Reserved.This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

APPENDIX
Methods beginning with a leading underscore are considered private and are intended for internal use by this module. They are not considered part of the public interface and are described here for documentation purposes only.

  blast_remote
 Usage     : @files = blast_remote( $blast_object,  %namedParameters);
           : This method is exported.
 Purpose   : Run a remote Blast analysis on one or more sequences.
           : NOTE: The name of this method is potentially misleading
           :       since the a local server could be specified.
           :       Probably should be called blast_http.
 Returns   : Array containing a list of filenames of the Blast reports.
 Argument  : First argument should be a Bio::Tools::Blast.pm object reference.
           : This object is primarily used for error reporting
           : Remaining arguments are named parameters:
           : (PARAMETER TAGS CAN BE UPPER OR LOWER CASE).
           :
           :   -ALIGN      => integer, number of alignments (B, 100)
           :   -ALIGN_VIEW => alignment view option (see below)
           :   -CUTOFF     => Blast score cutoff (60-110 or 'default')
           :   -DATABASE   => name of database (see below)
           :   -DESCR      => integer, number of on-line descriptions (V, 100)
           :   -EXPECT     => expect value cutoff
           :   -EXPECT_PSI => expect value for inclusion in PSI-BLAST iteration 1
           :   -FILTER     => sequence complexity filter ('default' or 'none')
           :   -GAP        => 'on' or 'off'
           :   -GAP_CREATE => gap creation penalty (G, 5)
           :   -GAP_EXTEND => gap extension penalty (E, 2)
           :   -GEN_CODE   => integer for special genetic code (see below) blastx only
           :   -GRAPH      => 'on' or 'off' (graphical overview not yet supported)
           :   -HISTOGRAM  => 'on' or 'off' or 'both'
           :   -HTML       => 'on' or 'off' or 'both'
           :   -INPUT_TYPE => 'Sequence in FASTA format' or 'Accession or GI'
           :   -MATRIX     => substitution scoring matrix (blast1 only for NCBI server)
           :   -NCBI_GI    => 'on' or 'off'
           :   -MATCH      => match reward (r, 1)       (blastn only)
           :   -MAX_LEN    => max query sequence length to blast
           :   -MIN_LEN    => min query sequence length to blast
           :   -MISMATCH   => mismatch penalty (q, -3)  (blastn only)
           :   -ORGANISM   => organism name to limit Blast2 search.
           :   -ORGANISM_CUSTOM  => custom organism or taxon name.
           :   -OUT_DIR    => output directory to store blast result files
           :   -PROG       => name of blast program (blastp, blastx, etc.)
           :   -SEQS       => ref to an array of Bio::Seq.pm objects.
           :   -SERVER     => blast server to use (default is NCBI Blast2)
           :   -STRAND     => Default = 'Both' (not used by NCBI servers)
           :   -VERSION    => blast version (1, 2, PSI, WashU)
           :   -WORD       => word size (W, 11 for blastn, 3 for all others)
#rnc:   LIST_ORG
#       valid list_org entries for blast2 are a string of 50 chars max, default is empty string
           :
 Throws    : Exception if:
           :   - Cannot obtain parameters by calling _rearrange() on the
           :     first argument, which should be a Bio::Tools::Blast.pm object ref.
           :   - No sequences are provided.
           :   - Sequence type is incompatible with Blast program type.
           :   - Database name is not one of the valid names.
           :   - Supplied e-mail address looks invalid.
 Comments  :
  -------------------------------------------------------------
  Available programs: blastn, blastx, dbest, blastp, tblastn, tblastx
  Program versions: 1, 2, PSI, WashU (or WU)
  -------------------------------------------------------------
  Available databases:
        nr, month, swissprot, dbest, dbsts,
        est_mouse, est_human, est_others, pdb, vector, kabat,
        mito, alu, epd, yeast, ecoli, gss, htgs.
    These are exported by this module in the @Blast_dbp_remote
    and @Blast_dbn_remote arrays.
  -------------------------------------------------------------
  Available Genetic Codes are (blastx only):
        (1) Standard                    (2) Vertebrate Mitochondrial
        (3) Yeast Mitochondrial         (4) Mold Mitochondrial; ...
        (5) Invertebrate Mitochondrial  (6) Ciliate Nuclear; ...
        (9) Echinoderm Mitochondrial    (10) Euplotid Nuclear
        (11) Bacterial                  (12) Alternative Yeast Nuclear
        (13) Ascidian Mitochondrial     (14) Flatworm Mitochondrial
        (15) Blepharisma Macronuclear
  -------------------------------------------------------------
  Available values for organism (Blast2):
      (None)   (DEFAULT; note that the parentheses are required.)
      Arabidopsis thaliana
      Bacillus subtilis
      Bos taurus
      Caenorhabditis elegans
      Danio rerio
      Dictyostelium discoideum
      Drosophila melanogaster
      Escherichia coli
      Gallus gallus
      Homo sapiens
      Human immunodeficiency virus type 1
      Mus musculus
      Oryctolagus cuniculus
      Oryza sativa
      Ovis aries
      Plasmodium falciparum
      Rattus norvegicus
      Saccharomyces cerevisiae
      Schizosaccharomyces pombe
      Simian immunodeficiency virus
      Xenopus laevis
      Zea mays
  -------------------------------------------------------------
  Available values for align_view (Blast2):
       0             Pairwise  (DEFAULT)
       1             master-slave with identities
       2             master-slave without identities
       3             flat master-slave with identities
       4             flat master-slave without identities
 -------------------------------------------------------------
  Available substitution scoring matrices (NCBI):
      BLAST2 matrices: BLOSUM80, BLOSUM62, BLOSUM45, PAM30, PAM70
      BLAST1 matrices: BLOSUM62, PAM40, PAM120, PAM250, IDENTITY.
      Others members of the BLOSUM and PAM family of matrices
      may be available as well.
      These are exported by this module in the @Blast_matrix_remote array.
      Note that certain combinations of matrices and gap creation/extension
      penalties are disallowed (E.g., PAM250 will work with 12/2 but not 11/1).
 --------------------------------------------------------------
   Limited values for gap creation and extension are supported for
   blastp, blastx, tblastn.  Some supported and suggested values are:
  Creation     Extension
     10             1
     10             2
     11             1
      8             2
      9             2
  -------------------------------------------------------------
  Available sequence complexity filters:
       SEG, SEG+XNU, XNU, dust, none.
See Also : _set_options(), _adjust_options(), _validate_options(), _blast(), Bio::Tools::Blast.pm

APPENDIX 2: Parameter listings
Parameters for Blast (NCBI ungapped, no longer supported by NCBI so should dicontinue use of ungapped blast), Blast2 (NCBI), PSI-Blast2 (NCBI). WashU-Blast2 has yet to be added as does PHI-Blast2 (NCBI).

These lists of parameters for posting to blast servers were obtained directly from the respective WWW forms for each server.

  Basic ungapped BLAST Search Server Parameters
PROGRAM [default value]:blastn
    blastp tblastn tblastx blastx

DATALIB [default value]:nr
    month swissprot dbest dbsts pdb vector kabat mito alu epd yeast gss htgs ecoli

INPUT_TYPE [default value]:Sequence in FASTA format
    Accession or GI

SEQUENCE

EXPECT [default value]:default
    0.0001 0.01 1 10 100 1000

CUTOFF [default value]:default
    60 70 80 90 100 110

MATRIX [default value]:default
    BLOSUM62 PAM40 PAM120 PAM250 IDENTITY

STRAND [default value]:both
    top bottom

FILTER [default value]:default none dust SEG SEG+XNU XNU

HISTOGRAM [default value]:'' HISTOGRAM

NCBI_GI [default value]:"" NCBI_GI

DESCRIPTIONS [default value]:default 0 10 50 100 250 500

ALIGNMENTS [default value]:default 0 10 50 100 250 500

ADVANCED [default value]:""

EMAIL [default value]:'' IS_SET

PATH [default value]:""

HTML [default value]:'' HTML

  Basic Blast 2
PROGRAM [default value]:blastn blastp blastx tblastn tblastx

DATALIB [default value]:nr month swissprot dbest dbsts est_mouse est_human est_others pdb pat vector kabat mito alu epd yeast ecoli gss htgs

UNGAPPED_ALIGNMENT [default value]:'' is_set

FSET [default value]:is_set ''

OVERVIEW [default value]:is_set ''

INPUT_TYPE [default value]:Sequence in FASTA format Accession or GI

SEQUENCE

EMAIL [default value]:'' IS_SET

PATH [default value]:""

HTML [default value]:'' IS_SET

  BLAST2 ADVANCED
PROGRAM [default value]:blastn blastp blastx tblastn tblastx

DATALIB [default value]:nr
 month swissprot dbest dbsts est_mouse est_human est_others pdb pat vector kabat mito alu epd yeast ecoli gss htgs

UNGAPPED_ALIGNMENT [default value]:"" is_set

INPUT_TYPE [default value]:Sequence in FASTA format Accession or GI

SEQUENCE

GI_LIST [default value]:(None) Arabidopsis thaliana Bacillus subtilis Bos taurus Caenorhabditis elegans Danio rerio Dictyostelium discoideum Drosophila melanogaster Escherichia coli Gallus gallus Homo sapiens Human immunodeficiency virus type 1 Mus musculus Oryctolagus cuniculus Oryza sativa Ovis aries Plasmodium falciparum Rattus norvegicus Saccharomyces cerevisiae Schizosaccharomyces pombe Simian immunodeficiency virus Xenopus laevis Zea mays

LIST_ORG

EXPECT [default value]:10 0.0001 0.01 1 10 100 1000

FILTER [default value]:default none

NCBI_GI [default value]:'' is_set

OVERVIEW [default value]:is_set ''

DESCRIPTIONS [default value]:500 0 10 50 100 250 500

ALIGNMENTS [default value]:500 0 10 50 100 250 500

ALIGNMENT_VIEW
[default value]:0    #Pairwise
1    #master-slave with identities
2    #master-slave without identities
3    #flat master-slave with identities
4    #flat master-slave without identities

GENETIC_CODE [default value]:Standard (1) Vertebrate Mitochondrial (2) Yeast Mitochondrial (3) Mold Mitochondrial; ... (4) Invertebrate Mitochondrial (5) Ciliate Nuclear; ... (6) Echinoderm Mitochondrial (9) Euplotid Nuclear (10) Bacterial (11) Alternative Yeast Nuclear (12) Ascidian Mitochondrial (13) Flatworm Mitochondrial (14) Blepharisma Macronuclear (15)

MAT_PARAM
[default value]:BLOSUM62     11     1
PAM30     9     1
PAM70     10     1
BLOSUM80     10     1
BLOSUM62     11     1
BLOSUM45     14     2
PAM30     7     2
PAM30     6     2
PAM30     5     2
PAM30     10     1
PAM30     9     1  #recommended
PAM30     8     1
PAM70     8     2
PAM70     7     2
PAM70     6     2
PAM70     11     1
PAM70     10     1  #recommended
PAM70     9     1
BLOSUM80     8     2
BLOSUM80     7     2
BLOSUM80     6     2
BLOSUM80     11     1
BLOSUM80     10     1  #recommended
BLOSUM80     9     1
BLOSUM62     9     2
BLOSUM62     8     2
BLOSUM62     7     2
BLOSUM62     12     1
BLOSUM62     11     1  #recommended
BLOSUM62     10     1
BLOSUM45     13     3
BLOSUM45     12     3
BLOSUM45     11     3
BLOSUM45     10     3
BLOSUM45     15     2
BLOSUM45     14     2  #recommended
BLOSUM45     13     2
BLOSUM45     12     2
BLOSUM45     19     1
BLOSUM45     18     1
BLOSUM45     17     1
BLOSUM45     16     1

OTHER_ADVANCED [default value]:""

EMAIL [default value]:'' IS_SET

PATH [default value]:""

HTML [default value]:'' IS_SET

  PSI BLAST2
PROGRAM [default value]:blastp

DATALIB [default value]:nr month swissprot pdb kabat alu yeast ecoli

GAPPED_ALIGNMENT [default value]:is_set ''

INPUT_TYPE [default value]:Sequence in FASTA format Accession or GI

SEQUENCE

EXPECT [default value]:10 0.0001 0.01 1 10 100 1000

FILTER [default value]:default none

NCBI_GI [default value]:'' is_set

GRAPHIC_OVERVIEW [default value]:is_set ''

DESCRIPTIONS [default value]:500 0 10 50 100 250 500

ALIGNMENTS [default value]:500 0 10 50 100 250 500

E_THRESH [default value]:0.001 #max value is 10

MAT_PARAM
[default value]:BLOSUM62     11     1
PAM30     9     1
 PAM70     10     1
 BLOSUM80     10     1
 BLOSUM62     11     1
 BLOSUM45     14     2
 PAM30     7     2
 PAM30     6     2
 PAM30     5     2
 PAM30     10     1
 PAM30     9     1
 PAM30     8     1
 PAM70     8     2
 PAM70     7     2
 PAM70     6     2
 PAM70     11     1
 PAM70     10     1
 PAM70     9     1
 BLOSUM80     8     2
 BLOSUM80     7     2
 BLOSUM80     6     2
 BLOSUM80     11     1
 BLOSUM80     10     1
 BLOSUM80     9     1
 BLOSUM62     9     2
 BLOSUM62     8     2
 BLOSUM62     7     2
 BLOSUM62     12     1
 BLOSUM62     11     1
 BLOSUM62     10     1
 BLOSUM45     13     3
 BLOSUM45     12     3
 BLOSUM45     11     3
 BLOSUM45     10     3
 BLOSUM45     15     2
 BLOSUM45     14     2
 BLOSUM45     13     2
BLOSUM45     12     2
BLOSUM45     19     1
BLOSUM45     18     1
BLOSUM45     17     1
BLOSUM45     16     1

OTHER_ADVANCED [default value]:""

  WashU BLAST2
WU-Blast2 Database Searches http://www2.ebi.ac.uk/blast2/

email ""

title Sequence

srchtype interactive email

database swall swissprot swnew trembl tremblnew pdb gpcrdb prints HLAprot embl emnew est igvec emvec imgt HLAnuc

program WU-blastp WU-blastx WU-blastn

matrix blosum62 blosum30 blosum35 blosum40 blosum45 blosum50 blosum65 blosum70 blosum75 blosum80 blosum85 blosum90 blosum100 GONNET pam10 pam20 pam30 pam40 pam50 pam60 pam70 pam80 pam90 pam100 pam110 pam120 pam130 pam140 pam150 pam160 pam170 pam180 pam190 pam200 pam210 pam220 pam230 pam240 pam250 pam260 pam270 pam280 pam290 pam300 pam310 pam320 pam330 pam340 pam350 pam360 pam370 pam380 pam390 pam400 pam410 pam420 pam430 pam440 pam450 pam460 pam470 pam480 pam490 pam500

strand default top bottom

exp default 1.0 10 100 1000

filter none seg xnu seg+xnu dust

echofilter no yes

histogram no yes

stats sump poisson

sort pvalue count highscore totalscore

scores default 5 10 20 50 100 150 200 250

numal default 5 10 20 50 100 150 200 250

sequence