ArticleThe FEBS journal2012
BioV Suite--a collection of programs for the study of transport protein evolution.
Article in The FEBS journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
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- The evolving biology of the proton-coupled folate transporter: New insights into regulation, structure, and mechanism.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2022Review
- Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species.Microbial physiology · 2022Article
- Discovery and Characterization of the Phospholemman/SIMP/Viroporin Superfamily.Microbial physiology · 2022Article
- Comparative analyses of transcriptional responses of Dectes texanus LeConte (Coleoptera: Cerambycidae) larvae fed on three different host plants and artificial diet.Scientific reports · 2021Article
- Comparative population genomic analyses of transporters within the Asgard archaeal superphylum.PloS one · 2021Article
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- Expansion of the Major Facilitator Superfamily (MFS) to include novel transporters as well as transmembrane-acting enzymes.Biochimica et biophysica acta. Biomembranes · 2020Article
- Systems Biology Analysis Reveals Eight SLC22 Transporter Subgroups, Including OATs, OCTs, and OCTNs.International journal of molecular sciences · 2020Article
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- Expansion of the Transporter-Opsin-G protein-coupled receptor superfamily with five new protein families.PloS one · 2020Article
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- Comparative genomics of the transportome of Ten Treponema species.Microbial pathogenesis · 2019Article
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2 authors.
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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].
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