Automat and BLAST: comparison of two protein sequence similarity search programs

Cantalloube, Hubert; Labesse, Gilles; Chomilier, Jacques; Nahum, Carole; Cho, Y. Y.; Chams, V.; Achour, Ahlem; Lachgar, A.; Mbika, J. P.; Issing, W.

doi:10.1093/bioinformatics/11.3.261

Cited by 6 publications

(5 citation statements)

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“…Owing to redundancy elimination by AUTOMAT, only CYSA_YERPS is listed in the output, at position 48, thus rendering human use of the listing easier. More detailed comparisons between AUTOMAT and BLAST have been presented elsewhere and have demonstrated the complementarity of the results produced by these two programs on proteins such as the RED (reductase-epimerase-dehydrogenase), HMP (haemoglobin-like protein of Escherichia coli ) and HIV-1 Env protein families (10). …”

Section: Automat: a Sequence Database Scanning Programmentioning

confidence: 96%

“…Its design makes it more systematic than BLAST. AUTOMAT and BLAST lead to complementary results in terms of analysing protein sequences (10). In brief, the query sequence is split into words of minimal length w chosen by the user, who can also define an alphabet of classes of equivalent amino acids.…”

Section: Automat: a Sequence Database Scanning Programmentioning

confidence: 99%

“…AUTOMAT has been the first software program to introduce histograms presenting the frequencies in the database of all the words of the query larger than w and to delete automatically redundant alignments originating from different sequences in the output listing (10,11). AUTOMAT and BLAST lead to coherent results for protein sequences in comparable computer time, but for nucleic acids AUTOMAT allows triggers w shorter (5 characters by default) than BLAST (words of 11 characters), thus leading to more sensitivity than BLAST.…”

Section: Automat: a Sequence Database Scanning Programmentioning

confidence: 99%

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RPBS: a web resource for structural bioinformatics

Alland¹,

Moreews²,

Boens³

et al. 2005

Nucleic Acids Research

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RPBS (Ressource Parisienne en Bioinformatique Structurale) is a resource dedicated primarily to structural bioinformatics. It is the result of a joint effort by several teams to set up an interface that offers original and powerful methods in the field. As an illustration, we focus here on three such methods uniquely available at RPBS: AUTOMAT for sequence databank scanning, YAKUSA for structure databank scanning and WLOOP for homology loop modelling. The RPBS server can be accessed at and the specific services at .

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Section: Automat: a Sequence Database Scanning Programmentioning

confidence: 96%

Section: Automat: a Sequence Database Scanning Programmentioning

confidence: 99%

Section: Automat: a Sequence Database Scanning Programmentioning

confidence: 99%

See 1 more Smart Citation

RPBS: a web resource for structural bioinformatics

Alland¹,

Moreews²,

Boens³

et al. 2005

Nucleic Acids Research

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“…The sequence of ZFERV Env was aligned using BLASTp [21]. The results showed that it was the member of HIV-1-like NHR and CHR superfamily while NHR region contained residues 468-505 and CHR region contained residues 535-543.…”

Section: Construction Of 3d Structures Of Nhr and Chr In Zferv Envmentioning

confidence: 99%

Characterization of the fusion core in zebrafish endogenous retroviral envelope protein

Shi

Zhang

Gong

et al. 2015

Biochemical and Biophysical Research Communications

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Zebrafish endogenous retrovirus (ZFERV) is the unique endogenous retrovirus in zebrafish, as yet, containing intact open reading frames of its envelope protein gene in zebrafish genome. Similarly, several envelope proteins of endogenous retroviruses in human and other mammalian animal genomes (such as syncytin-1 and 2 in human, syncytin-A and B in mouse) were identified and shown to be functional in induction of cell-cell fusion involved in placental development. ZFERV envelope protein (Env) gene appears to be also functional in vivo because it is expressible. After sequence alignment, we found ZFERV Env shares similar structural profiles with syncytin and other type I viral envelopes, especially in the regions of N- and C-terminal heptad repeats (NHR and CHR) which were crucial for membrane fusion. We expressed the regions of N + C protein in the ZFERV Env (residues 459-567, including predicted NHR and CHR) to characterize the fusion core structure. We found N + C protein could form a stable coiled-coil trimer that consists of three helical NHR regions forming a central trimeric core, and three helical CHR regions packing into the grooves on the surface of the central core. The structural characterization of the fusion core revealed the possible mechanism of fusion mediated by ZFERV Env. These results gave comprehensive explanation of how the ancient virus infects the zebrafish and integrates into the genome million years ago, and showed a rational clue for discovery of physiological significance (e.g., medicate cell-cell fusion).

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“…Alignment of amino acid sequences was performed using the program Bl2seq, a new computer program for creating alignments of two protein sequences 24 .…”

Section: Sequence Alignmentmentioning

confidence: 99%

Biochemical characterization of the δ-carbonic anhydrase from the marine diatomThalassiosira weissflogii, TweCA

Prete

Vullo

Luca

et al. 2014

Journal of Enzyme Inhibition and Medicinal Chemistry

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Diatom genome sequences clearly reveal the presence of different systems for HCO 3 À uptake. Carbon-concentrating mechanisms (CCM) based on HCO 3 À transport and a plastid-localized carbonic anhydrase (CA, EC 4.2.1.1) appear to be more probable than the others because CAs have been identified in the genome of many diatoms. CAs are key enzymes involved in the acquisition of inorganic carbon for photosynthesis in phytoplankton, as they catalyze efficiently the interconversion between carbon dioxide and bicarbonate. Five genetically distinct classes of CAs exist, a-, b-, g-, d-and z and all of them are metalloenzymes. Recently we investigated for the first time the catalytic activity and inhibition of the d-class CA from the marine diatom Thalassiosira weissflogii, named TweCA. This enzyme is an efficient catalyst for the CO 2 hydration and its inhibition profile with sulfonamide/sulfamate and anions have also been investigated. Here, we report the detailed biochemical characterization and chemico-physical properties of the d-CA of T. weissflogii. The d-CA encoding gene was cloned and expressed in Artic Express cells and the recombinant protein purified to homogeneity. Interesting to note that TweCA has no intrinsic esterase activity with 4-nitrophenyl acetate (pNpA) as substrate although the phylogenetic analysis showed that d-CAs are closer to the a-CAs than to the other classes of such enzymes.

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Automat and BLAST: comparison of two protein sequence similarity search programs

Cited by 6 publications

References 0 publications

RPBS: a web resource for structural bioinformatics

RPBS: a web resource for structural bioinformatics

Characterization of the fusion core in zebrafish endogenous retroviral envelope protein

Biochemical characterization of the δ-carbonic anhydrase from the marine diatomThalassiosira weissflogii, TweCA

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