Download Shareware and Freeware Software for Windows, Linux, Macintosh, PDA

line Home  |  About Us  |  Link To Us  |  FAQ  |  Contact

Serving Software Downloads in 976 Categories, Downloaded 29.888.196 Times

Peptide::Pubmed 1.02

  Date Added: October 08, 2010  |  Visits: 639

Peptide::Pubmed

Report Broken Link
Printer Friendly Version


Product Homepage
Download (75 downloads)



Peptide::Pubmed is a Perl module that can extract peptide sequences from MEDLINE article abstracts. SYNOPSIS use Peptide::Pubmed; $parser = Peptide::Pubmed->new; $in = { PMID => q[15527327], Author => q[Doe JJ, Smith Q], Journal => q[J Biological Foo. 2004;8(2):123-30.], Title => q[Foo, bar and its significance in phage display.], Abstract => q[Peptide sequences EYHHYNK and Arg-Gly-Asp, but not ACCCGTNA or VEGFRI.], Mesh => q[Genes, p53/genetics; Humans; Bar], Chemical => q[Multienzyme Complexes; Peptide Library; Foo], }; $parser->parse_abstract($in); # get the peptide sequences in 1 letter symbols (select all words where the # combined word/abstract score is above threshold: # WordAbstScore >= WordAbstScoreMin): @seqs = $parser->get_seqs; print "@seqsn"; # prints: EYHHYNK RGD EXAMPLES # same as above, set threshold explicitly: $parser->WordAbstScoreMin(0.4); @seqs = $parser->get_seqs; # set low threshold to get more peptide sequences (but at a cost of getting # more false positives) $parser->WordAbstScoreMin(-1); @seqs = $parser->get_seqs; print "@seqsn"; # prints: EYHHYNK RGD ACCCGTNA VEGFRI # reset threshold back: $parser->WordAbstScoreMin(0.4); # get more data for the abstract: $abst = $parser->get_abst; print "$abst->{AbstScore}n"; # abstract score, in the [0,1] interval print "$abst->{AbstMtext}n"; # abstract with sequences marked up: # Peptide sequences EYHHYNK and Arg-Gly-Asp, # but not ACCCGTNA or VEGFRI. # get more data for the words, in addition to peptide sequences: @words = $parser->get_words; for my $word (@words) { # combined word/abstract score, in the [0,1] interval print "$word->{WordAbstScore}n"; # word as found in the abstract, eg Arg-Gly-Asp, print "$word->{WordOrig}n"; # peptide sequence in 1 letter symbols, eg RGD print "$word->{WordSequence}n"; } # There are no mandatory input fields. This will work too, but may give lower score. $in = { Abstract => q[Peptide sequences EYHHYNK and Arg-Gly-Asp, but not ACCCGTNA or VEGFRI.], }; $parser->parse_abstract($in); @words = $parser->get_words; # No peptide sequences are found in empty input: $in = undef; $parser->parse_abstract($in); @words = $parser->get_words;.

Requirements: No special requirements
Platforms: Linux
Keyword: Abstract Acccgtna Eyhhynk Medline Peptide Peptide Sequences Peptidepubmed Perl Module Print Rgd Sequences Wordabstscoremin Words
Users rating: 0/10

License: Freeware Size: 358.4 KB
USER REVIEWS
More Reviews or Write Review


PEPTIDE::PUBMED RELATED
Libraries  -  MassSpec::ViewSpectrum::RealVsHypPeptide 0.02
MassSpec::ViewSpectrum::RealVsHypPeptide is a Perl module to view a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico. SYNOPSIS use MassSpec::ViewSpectrum::RealVsHypPeptide; open...
8.19 KB  
Libraries  -  DBIx::SQL::Abstract 0.07
DBIx::SQL::Abstract is a Perl module that provides a convenient abstraction layer to a database. SYNOPSIS use DBIx::SQL::Abstract; my $dbh = DBIx::SQL::Abstract->new( %dbcfg ); Building SQL Abstractions. my($query, @bind) =...
4.1 KB  
Libraries  -  Data::Phrasebook::Loader::XML 0.12
Data::Phrasebook::Loader::XML Perl module can abstract your phrases with XML. SYNOPSIS use Data::Phrasebook; my $q = Data::Phrasebook->new( class => Fnerk, loader => XML, file => phrases.xml, dict => Dictionary, # optional ); OR my...
17.41 KB  
Libraries  -  CPAN::Cache 0.02
CPAN::Cache is a Perl module abstract locally-cached logical subset of a CPAN mirror. There have been any number of scripts and modules written that contain as part of their functionality some form of locally stored partial mirror of the CPAN...
21.5 KB  
Libraries  -  CORBA::IDLtreev 1.4
CORBA::IDLtree is a Perl module that builds abstract syntax trees from CORBA IDL. The main export is sub Parse_File which takes an IDL input file name as the parameter, and returns a reference to an array of references to the root nodes...
36.86 KB  
Entertainment  -  Abstract Media 1.0
Introducing Augmented Reality (AR) from Abstract Media. Using cutting edge technology, 3D objects and animations appear in real 3D space right before your eyes! Simply grab an Abstract Business card from one of our team members or print out...
54.4 MB  
Libraries  -  Convert::GeekCode 0.51
Convert::GeekCode is a Perl module that can convert and generate geek code sequences. SYNOPSIS use Convert::GeekCode; # exports geek_decode() my @out = geek_decode(q( -----BEGIN GEEK CODE BLOCK----- Version: 3.12...
25.6 KB  
Libraries  -  Term::ANSIScreen 1.42
Term::ANSIScreen is a Perl module for terminal control using ANSI escape sequences. SYNOPSIS # qw/:color/ is exported by default, i.e. color() & colored() use Term::ANSIScreen qw/:color :cursor :screen :keyboard/; print setmode(1),...
15.36 KB  
Libraries  -  Apache::Wyrd 0.94
Apache::Wyrd is a Perl module for HTML embeddable perl objects under mod_perl. Apache::Wyrd is the core module in a collection of interoperating modules that allow the rapid object-oriented development of web sites in Apaches mod_perl...
174.08 KB  
Libraries  -  Audio::File::AudioProperties 0.10
Audio::File::AudioProperties is a Perl module that can abstract an audio files audio properties. Audio::File::AudioProperties is the base class for other file format independant audio property classes like Audio::File::Flac::AudioProperties or...
74.75 KB  
NEW DOWNLOADS IN PROGRAMMING, LIBRARIES
Programming  -  FLEX-db Digital Asset Manager 3.0.9
FLEX-db - an enterprise Digital Asset Manager (DAM). It ingests and links metadata with files, creates thumbnails, and processes files using business rules. FLEX-db has a JSP client, Java app server for file input and output and an EJB metadata...
21.57 MB  
Programming  -  Libicom 0.9.0
The libicom library is a character based dynamicly linked library for Linux. It is used to remotely control the Icom IC-R8500 wide band receiver via an RS232 link. All call and return parameters to the control functions are character string based....
20.48 KB  
Programming  -  dotdesktop 0.3
Dotdesktop library provides ability to parse desktop entry file and access the information in a convenient way. Desktop entry file format is defined by freedesktop.org, it is used to describe information about an application such as the name and...
327.68 KB  
Programming  -  Cedalion for Linux 0.2.6
Cedalion is a programming language that allows its users to add new abstractions and define (and use) internal DSLs. Its innovation is in the fact that it uses projectional editing to allow the new abstractions to have no syntactic limitations.
471.04 KB  
Programming  -  libyasl 0.2
Libyasl is a C++ class library to easily realize TCP/UDP/Multicast clientsand servers in IPv4 and IPv6 environments under GNU/Linux systems.
143.36 KB  
Libraries  -  wolfSSL 3.11.0
The wolfSSL embedded SSL/TLS library is a lightweight SSL library written in ANSI standard C and targeted for embedded and RTOS environments - primarily because of its small size, speed, and feature set. It is commonly used in standard operating...
2.73 MB  
Libraries  -  EuGTK 4.8.9
Makes it easy to develop good- looking, fast, cross-platform programs that run on Linux, OS X, and Windows. Euphoria is a very fast interpreted/compiled language with straight-forward syntax. EuGTK allows programming in a clean, object-oriented...
10.68 MB  
Libraries  -  Linux User Group Library Manager 1.0
The LUG Library Manager is a project to help Linux User Groups start their own library. A LUG library is helpful to the community at large because it increases access to information, and gives everyone the opportunity to become more knowledgeable.
5.35 KB  
Libraries  -  Module::MakefilePL::Parse 0.12
Module::MakefilePL::Parse is a Perl module to parse required modules from Makefile.PL. SYNOPSIS use Module::MakefilePL::Parse; open $fh, Makefile.PL; $parser = Module::MakefilePL::Parse->new( join("", ) ); $info = $parser->required;...
8.19 KB  
Libraries  -  sqlpp 0.06
sqlpp Perl package is a SQL preprocessor. sqlpp is a conventional cpp-alike preprocessor taught to understand SQL ( PgSQL, in particular) syntax specificities. In addition to the standard #define/#ifdef/#else/#endif cohort, provides also...
10.24 KB