Premium
BioV Suite – a collection of programs for the study of transport protein evolution
Author(s) -
Reddy Vamsee S.,
Saier Milton H.
Publication year - 2012
Publication title -
the febs journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 204
eISSN - 1742-4658
pISSN - 1742-464X
DOI - 10.1111/j.1742-4658.2012.08590.x
Subject(s) - computer science , suite , python (programming language) , scripting language , computational biology , proteome , sequence alignment , genome , multiple sequence alignment , data mining , theoretical computer science , bioinformatics , biology , programming language , peptide sequence , genetics , gene , history , archaeology
The Bio‐V Suite is a collection of Python scripts designed specifically for bioinformatic research regarding transport protein evolution. The Bio‐V Suite contains nine powerful programs for Unix‐based environments, each of which can be run as a standalone tool or be accessed in a programmatic manner. These programs and their functions are as follows. The transmembrane alpha‐helical statistical prediction tool (TMStats) generates topological statistics for transport proteins. The Global Sequence Alignment Tool (GSAT) performs shuffle‐based binary alignments and is fully scalable. It can cross‐compare two FASTA files or individual sequences. Protocol1 performs remote PSI‐Blast searches and filters redundant/similar sequences and annotates them. Protocol2 finds homologues between FASTA lists and generates graphical reports. The Targeted Smith–Waterman Search (TSSearch) uses a rapid search algorithm to find distant homologues in FASTA files in a heuristic manner. SSearch is the exhaustive version of TSSearch. Genome‐Blast (GBlast) will identify potential transport proteins in any genome/proteome file or find similar transport protein homologues between two different genomes/proteomes before generating a graphical report. AncientRep (AR) will find putative transmembrane repeat units using a list of homologues. DefineFamily (DF) will generate a FASTA list to represent an entire Transporter Classification family. These nine programs are tabulated with descriptions of their capabilities in Table 1. 1 Programs developed for studies of transport protein evolution but useful for the analysis of other protein (and nucleic acid) classes.Program Task performedTMStats Creates graphical charts to represent topological statistics within any TC hierarchy or FASTA file GSAT Provides a simple, shuffle‐based global alignment tool for detecting distant homologies Protocol1 Performs remote PSI‐BLAST searches with iterations using the NCBI NR database Protocol2 Compares two different families of transport proteins to find similarities. It uses TSSearch and SSearch and generates easy‐to‐read graphical reports TSSearch Uses a heuristic local search algorithm for rapid comparison of two different FASTA files and find similarities between them SSearch Uses a simple, exhaustive shuffle‐based local search algorithm to compare two different FASTA files and find their similarities GBlast Provides a search tool designed to identify potential transporters within entire genomes/proteomes. It generates easy‐to‐read graphical reports AncientRep Provides a horizontal or vertical search approach to find transmembrane repeat units within a list of homologues DefineFamily Generates a FASTA list to represent any TC family