Related Experiment Video
Updated: May 22, 2026

A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
BioV Suite--a collection of programs for the study of transport protein evolution
Vamsee S Reddy1, Milton H Saier
1Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, USA.
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 (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. [Table: see text].
Related Concept Videos
Evolutionary Relationships through Genome Comparisons
Overview of Protein Sorting and Transport
Protein sorting can be of two types: signal-based sorting and vesicle-based trafficking. In signal-based sorting, specific amino acid sequences called sorting signals target proteins to the proper location inside the cell either via gated transport or by protein translocation. In gated transport, folded...
Multi-pass Transmembrane Proteins and β-barrels
α-Helix containing multi-pass transmembrane proteins
Multi-pass transmembrane proteins such as G-protein-linked receptors (GPCRs) and...
The Significance of Membrane Transport
Transporters facilitate either an active or passive movement of solutes. They can allow a single-molecule transport down its...
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Applications of Molecular Taxonomy

