Saturday, August 9, 2008

Bioinformatics CPAN Modules / Bioinformatics CPAN Modules




Visit 123Bioinformatics.com for more Updates.



Bioperl is the product of a community effort
to produce Perl code which is useful in biology.

Bioperl Tutorial...

Bio::Tools::Run::PiseApplication::bambe

BAMBE Bayesian Analysis in Molecular
Biology and Evolution.

Bio::Tools::HMM
Perl extension to perform Hidden Markov
Model calculations.

Bio::Grep
Perl extension for searching in DNA and
Protein sequences.

Bio::Emboss
Write EMBOSS programs in Perl. This module
allows Perl programmers to access functions
of the EMBOSS (European Molecular Biology
Open Software Suite) package.

ncbinr2phenyxfasta.pl
Tranfoorm ncbirn bank into fasta with
annotated headers.

BLASTaid
A simple interface for byte indexing a
WU-BLAST multi-part report for
faster access.This module was written
to aid accessing specific reports from longer,
multi part WU-BLAST (http://blast.wustl.edu/)
alignments reports.

Bio::Tools::Run::PiseApplication::fasta
Bioperl class for FASTA Sequence database search.

Peptide::Pubmed
Extract peptide sequences from MEDLINE article abstracts.

ONTO-PERL
'ONTO-PERL' a collection of perl modules for dealing
with the Cell Cycle Ontology (CCO) and in general
with OBO ontologies (like the Gene Ontology).

FASTAParse
A light-weight parsing module for handling FASTA
formatted sequence within larger perl applications.

Bio::DB::SwissProt
Database object interface to SwissProt retrieval.

Bio::Tree::DistanceFactory
Construct a phylogenetic tree using distance based
methods.

Bio::Tree::Compatible
Testing compatibility of phylogenetic trees with
nested taxa.

Bio::Seq::Quality
Implementation of sequence with residue quality
and trace values.

Microarray
A Perl module for creating and manipulating DNA
Microarray experiment objects.

uniprotdat2fasta.pl
converts uniprot native text format (.dat or .seq)
into fasta file,reporting varsplic,signal,peptide,PTM,conflicts.

fasta-shuffle-notryptic.pl
Reads input fasta file and produce a shuffle
databank & avoid known cleaved peptides: shuffle
sequence but avoid producing known tryptic peptides.

Bio::Tools::Blast
Bioperl BLAST sequence analysis object.

Bio::Tools::Run::Alignment::Clustalw
Object for the calculation of a multiple sequence
alignment from a set of unaligned sequences or
alignments using the Clustalw program.

Bio::DB::EUtilities
Interface for handling web queries and data retrieval
from Entrez Utilities at NCBI.

Bio::Tools::Run::Alignment::TCoffee
Object for the calculation of a multiple sequence
alignment from a set.

Bio::Tools::Run::Alignment::Amap
Object for the calculation of an iterative multiple
sequence alignment from a set of unaligned sequences
or alignments using the Amap (2.0). program of
unaligned sequences or alignments using the TCoffee program.

Bio::Tools::Run::Primer3
Create input for and work with the output from the program
primer3.

Bio::Tools::Run::Seg
Object for identifying low complexity regions in a given
protein sequence.

Bio::Tools::Run::RepeatMasker
Wrapper for RepeatMasker Program.

Bio::Tools::Run::Pseudowise
Object for predicting 'pseudogenes' in a given sequence
given a protein and a CDNA sequence.

Bio::Tools::Run::Promoterwise
Wrapper for aligning two sequences using promoterwise.

Bio::Tools::Run::PiseApplication::stssearch
Searches a DNA database for matches with a set of STS
primers (EMBOSS).

Bio::Tools::Analysis::Protein::GOR4
wrapper around GOR4 protein secondary structure
prediction server.

Bio::Tools::Analysis::Protein::HNN
wrapper around HNN protein secondary structure prediction
server.

Bio::Tools::Analysis::Protein::Sopma
Wrapper around Sopma protein secondary structure prediction
server.

Bio::Tools::Run::Phylo::Phylip::Neighbor
Wrapper for the phylip program neighbor for creating a
phylogenetic tree(either through Neighbor or UPGMA) based
on protein distances based on amino substitution rate.

Bio::Align::ProteinStatistics
Calculate Protein Alignment statistics (mostly distances).

Bio::Tools::Prepeat
Finding repeats in protein sequences.

Bio::Tools::Analysis::Protein::Scansite
Wrapper around the Scansite server.

Bio::Tools::OddCodes
Object holding alternative alphabet coding for one
protein sequence.

make_mrna_protein
Convert an input mRNA/cDNA sequence into protein.

Chemistry::File::PDB
Protein Data Bank file format reader/writer.

Bio::Tools::Analysis::Protein::ELM
This module is a wrapper around the ELM server (http://elm.eu.org/)
which predicts short functional motifs on amino acid sequences.

Bio::Tools::Analysis::Protein::Mitoprot
Wrapper around Mitoprot server.

Bio::Tools::Run::Genewise
Object for predicting genes in a given sequence given a protein.

Bio::Tools::Run::Tmhmm
Object for identifying transmembrane helixes in a given
protein seequence.

Bio::SeqFeature::Gene::GeneStructure
A feature representing an arbitrarily complex structure
of a gene.

GO::AnnotationProvider::AnnotationParser
Parses a gene annotation file.

GO::OntologyProvider::OboParser
Provides API for retrieving data from Gene Ontology obo file.

Bio::SAGE::Comparison
Compares data from serial analysis of gene expression
(SAGE) libraries.

5 comments:

Cesar said...

Cool and useful site!
I saw your site because SciLink
I am Cesar Alvarez, and I wrote to you because some script in perl
I used to write script perl (I am a rockie in programing) like this
#!/usr/bin/perl -w
etc
but recently I saw a script in this way
perl -ne 'BEGIN {$column = 0}'

It is the same Perl? what are the rules for programing in this way?

Thank you!

I start a blog, the goal is that my partners in the lab were involved in basic bioinformatics, I hope that you could advise us!

Cesar Alvarez

Rakesh K Shardiwal said...

No perl doesn't have any special rules.

the line you saw is just a inline programming without creating file, he executed a block of statement in command line it self.

example:

perl -e 'print "Hello";'

Arguments to perl can alter how Perl processes input. For a complete list of these invocation options
-e specifies Perl expressions.
-p loops over and prints input.
-n loops over and does not print input.
-l strips newlines on input, and adds them on output.
-i causes perl to operate on files in-place, and optionally also backs up the files via -i.bak or whatever.
-a enables auto-split of input into the @F array.

and many more.

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