Search Results for "bioperl"
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Showing 15 open source projects for "bioperl"
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BioUtils Perl Library
A collection of Perl modules for handling fasta/q sequences and files.
WARNING: BioUtils has been migrated to Github (Nov 2017). For the most up-to-date versions and info please visit: https://github.com/islandhopper81/BioUtils BioUtils are a collection of Perl modules for DNA sequence analysis in bioinformatics. BioUtils is a significantly faster and more memory efficient alternative to BioPerl. However, it's functionality is currently limited to the features listed below. -
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BamBam
Tools for genomic analysis
BamBam includes numerous tools for analyzing DNA next-generation sequencing data. Tools are provided for calling SNPs and indels, identifying large scale deletions, tabulating counts of mapped reads, methylation analysis, and more. Depends on SAMtools (http://samtools.sourceforge.net/) and BAMtools (https://github.com/pezmaster31/bamtools). Also uses BioPerl, which is included in the download tarball. -
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GenTaxo
A perl script for comparative genomics
Requirements: Bioperl NCBI blast+ Usage: perl GenTaxo.pl -ani_files (files separeted by , without space) -aai_files (files separeted by , without space) -evalue (default: 0.001) -threads (default: 1) -verbose (default: False) -min_id (default: 30) -min_cov (default: 0.7) -min_seqs (default: 100) -karlin_files (files separeted by , without space) -output (default: Karlin_Distances.tsv) -verbose (default: False) -
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kmer_multi_sequence
returns counts of any kmer length from fastaA format input sequence(s)
Uses Bioperl SeqIO to parse fastA input and outputs kmer counts of a user determined length -
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5
DNATweezer
A suite of BioPerl wrappers for manipulating DNA and protein sequences
DNATweezer is a suite of Perl scripts for manipulating DNA and proteins sequences. These scripts provide command-line access to the most frequently used BioPerl DNA object methods e.g. reverse-complement and translation of DNA sequences, slicing a sequence alignment, rerooting a phylogenetic tree, and calculating diversity of a population of DNA sequences. -
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A tool to compare microbial genomes by their sequence fragments. We redistributed the Bioperl package in our software for convenience purpose. The latest Bioperl package can be downloaded from: http://www.bioperl.org. System Requirement: Java Runtime Environment 1.6.0 or above; Perl 5.0 or above If you have any difficulties to run this tool, just let me know by chenh12@nyumc.org.
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FastAlign.pl
FastAlign is a perl script which uses the heuristic method of tfasty
FastAlign.pl provides a more intuitive output to find exon-intron junctions. The query string is in amino acids and the hit string is in nucleotides. There are extra nucleotides at the end of the hit string (option -diff and by default = 10), that allow to verify if the intron start with common rules (5'-GTGCGA-... for group II intron and after an exonic T for group I intron). If you have Emboss, you can genarate a graphic with option -graph 1. Dependencies: - Perl - Bioperl - UNIX system... -
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BioPerl implemented in JavaScript. The library aims to promote and aid the development of bioinformatics applications in JavaScript much the same way as BioPerl helps bioinformatics development in Perl.
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LABnovo offers a method for laboratory housekeeping by correlating the lab processes that ultimately lead to the production of sequences. The metadata collected enables further data-mining in a community-centric environment.
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Biospha is a suite of perl scripts based on bioperl toolkit intended to help researches to manage large sequence file. With BIOSPHA you can classify each sequence according to the NCBI taxonomy. You also can get all taxonomic info from a GI or Taxid.
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Modware is an easy to use Perl library for querying and modifying genomic data in a Chado database. It provides a powerful link between BioPerl and Chado. This Chado API provides an intutitive way to use Chado from Perl.
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IISA - Intelligent Interface to Sequence Analysis is an expert system for biological sequence analysis using Bioperl and Prolog.
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Bioinformatic C++ library providing a central engine to other bio* libraries (BioPerl, BioPython, BioJava).
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14
Cis-Regulatory analysis modules. Includes frequenc/weight matrices scanning at genome level, annotation by using DB access to ensembl, genekeydb, etc. and visualization (through Bioperl or as custom UCSC tracks). May include gene set analysis in future.
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15
Find restriction enzymes that help differ known homologe DNA sequences (RFLP). Simulate electrophoresis gels. Usefull to investigate the diversity of a population by one of their common genes. Written in perl, uses bioperl modules and the GD library.
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