BLAST options, setting and defaults
...arately search protein or DNA databases. BLAST is best used for sequence sim...yield different results from BLAST, and may be useful for motif...w of BLAST, see the NCBI BLAST Course. Additional informatio...penalty for a mismatch in the blast portion of run [integer] default...2000 days ago
genoPlotR - plot gene and genome maps project!
genoPlotR is a R package to produce reproducible, publication-grade graphics of gene a...from usual format such as protein table files and blast results, as well as home-made...xample) Reads from common formats: Genbank, EMBL, blast, Ma...1998 days ago
1998 days ago
SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) wit...1998 days ago
Biotite: A general framework for computational biology
The package is open source and freely available at GitHu...onsists of four sub packages: sequence, structure, databases, and application. The se... database downloads files from the other databases such as RCSB PDB, and ap...1993 days ago
1972 days ago
1969 days ago
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a...gns putative functions to gene calls using protein-, virus-, and phage-centric databases.1844 days ago
TwinBLAST: When Two Is Better than One
TwinBLAST is a web-based tool for viewing 2 BLAST reports simultaneouslyside-by-side. It uses ExtJ...s. BioPerl (www.bioperl.org) is used to indexraw BLAST reports and Bio::Graphics is used to draw pictograms of the BLASThits...1729 days ago
phyloXML: XML for evolutionary biology and comparative genomics
phyloXML (example) is an XML language designed to describe phylogenet...standardized elements allows interoperability between various applications and databases. Furthermore, both due to ext...1637 days ago