Search results for "dist:BioPerl-Run Bio::SeqI"
Bio::Tools::Run::Mdust - Perl extension for Mdust nucleotide filtering
Perl wrapper for the nucleic acid complexity filtering program mdust as available from TIGR via <http://www.tigr.org/tdb/tgi/software/>. Takes a Bio::SeqI or Bio::PrimarySeqI object of type DNA as input. If a Bio::Seq::RichSeqI is passed then the low...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Hmmer - Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch
Wrapper module for Sean Eddy's HMMER suite of program to allow running of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam and hmmsearch. Binaries are available at http://hmmer.janelia.org/ You can pass most options understood by the command-line p...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Match - Wrapper for Transfac's match(TM)
This is a wrapper for running the match(TM) program supplied with Transfac Pro distributions. You can try supplying normal match command-line arguments to new(), eg. new(-b => 1) or calling arg-named methods (excluding the initial hyphens, eg. $facto...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::DB::SoapEUtilities - Interface to the NCBI Entrez web service *BETA*
This module allows the user to query the NCBI Entrez database via its SOAP (Simple Object Access Protocol) web service (described at <http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/DOC/esoap_help.h tml>). The basic tools ("einfo, esearch, eli...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::RepeatMasker - Wrapper for RepeatMasker Program
To use this module, the RepeatMasker program (and probably database) must be installed. RepeatMasker is a program that screens DNA sequences for interspersed repeats known to exist in mammalian genomes as well as for low complexity DNA sequences. For...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Alignment::Gmap - Wrapper for running gmap.
Bioperl-run wrapper around gmap. See <http://www.gene.com/share/gmap/> for information about gmap. It requires a reference to an array of bioperl SeqI objects and returns a reference to a filehandle from which the gmap output can be read. One can exp...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Alignment::Sim4 - Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences
Sim4 program is developed by Florea et al. for aligning cdna/est sequence to genomic sequences 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):96...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Alignment::MSAProbs - Object for the calculation of a multiple sequence alignment (MSA) from a set of unaligned sequences using the MSAProbs program
MSAProbs is Liu, Schmidt, and Maskell's (2010) alignment program using HMM and partition function posterior probabilities. For more a more in-depth description see the original publication: Liu, Y., Schmidt, B., and Maskell, D. L. (2010) MSAProbs: mu...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC