BioV Suite--a collection of programs for the study of transport protein evolution.

The FEBS Journal
Vamsee Reddy, Milton H Saier

Abstract

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...Continue Reading

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Mar 31, 2012·The FEBS Journal·Vamsee S ReddyMilton H Saier

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Citations

May 8, 2013·BMC Microbiology·Wei Hao ZhengMilton H Saier
Apr 22, 2014·Microbial Pathogenesis·Fengyi Tang, Milton H Saier
Nov 8, 2015·Nucleic Acids Research·Milton H SaierGabriel Moreno-Hagelsieb
Nov 15, 2013·Nucleic Acids Research·Milton H SaierAke Västermark
Mar 31, 2012·The FEBS Journal·Vamsee S ReddyMilton H Saier
Aug 29, 2013·The FEBS Journal·Daniel C YeeMilton H Saier
Jul 22, 2014·Proteins·Ake VastermarkMilton H Saier
Aug 8, 2014·The Journal of Eukaryotic Microbiology·Ujjwal Kumar, Milton H Saier
Aug 8, 2015·Microbial Pathogenesis·Bora Buyuktimkin, Milton H Saier
Jul 17, 2013·Biochimica Et Biophysica Acta·Bhaskara L Reddy, Milton H Saier
Jun 15, 2016·Microbial Pathogenesis·Bora Buyuktimkin, Milton H Saier
Nov 18, 2017·Journal of Molecular Microbiology and Biotechnology·Gabriel Moreno-HagelsiebMilton H Saier
Dec 6, 2018·PloS One·Hassan Zafar, Milton H Saier
Sep 1, 2014·Molecular Informatics·Shalini SaxenaDharmarajan Sriram
Dec 7, 2017·Journal of Molecular Microbiology and Biotechnology·Fereshteh Heidari TajabadiMilton H Saier
Mar 11, 2020·International Journal of Molecular Sciences·Darcy C EngelhartSanjay K Nigam
Dec 30, 2014·Physiological Reviews·Sanjay K NigamWei Wu
Mar 25, 2020·Biochimica Et Biophysica Acta. Biomembranes·Steven C WangMilton H Saier

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