MyHits: improvements to an interactive resource for analyzing protein sequences

Pagni, Marco; Ioannidis, Vassilios; Cerutti, Lorenzo; Zahn-Zabal, Monique; Jongeneel, C. Victor; Hau, Jörg; Martin, Olivier; Kuznetsov, Dmitry; Falquet, Laurent

doi:10.1093/nar/gkm352

Cited by 200 publications

(155 citation statements)

References 27 publications

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“…Reciprocally, similarly executed searches initiated with a multiple alignment of pannexins recovered LRRC8 proteins as the best hit (1.2e-08). In addition, HMMER v2 and PFSEARCH [12] searches conducted at MyHits [13] yielded the same hits and highly significant e-values. The direct contrast of the independent alignments of LRRC8s and pannexins using the profile-profile comparison HHALIGN 1.5.1.1 program [14] resulted in an e-value of 9.5e-08.…”

Section: Introductionmentioning

confidence: 67%

LRRC8 proteins share a common ancestor with pannexins, and may form hexameric channels involved in cell‐cell communication

2012

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Leucine-rich repeat-containing 8 (LRRC8) proteins are composed of four transmembrane helices and 17 leucine-rich repeats (LRR). Although LRRC8 proteins have been associated with important processes, like maturation of B cells or adipocyte differentiation, their biology and molecular function are largely unknown. We found that LRRC8 proteins originated from the combination of a pannexin and an LRR domain (most likely related to the SHOC2, LAP, RSU1 and LRRIQ4 protein families) before the diversification of chordates. We propose that, like pannexins, LRRC8 proteins form hexameric channels, which participate in cell-cell communication processes. According to the inferred topological model, and contrary to what was previously assumed, the six LRR domains are located in the cytoplasm, and could participate in the organisation of signalling cascades. By compiling available proteomics and gene expression data, and on the basis of the LRRC8 proposed hexameric channel structure, we present clues to the function of this family.

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Section: Introductionmentioning

confidence: 67%

LRRC8 proteins share a common ancestor with pannexins, and may form hexameric channels involved in cell‐cell communication

2012

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“…The Motif Scan of MyHits (http://myhits.isb-sib.ch/cgi-bin/ motif_scan) (Pagni et al, 2007) identifies sequence motifs. This tool can use eight motif databases (perox, hamap, pat, freq_pat, prf, pre, pfam_fs, and pfam_ls; Pagni et al, 2007) to perform predictions.…”

Section: Motif Scan Of Myhitsmentioning

confidence: 99%

“…This tool can use eight motif databases (perox, hamap, pat, freq_pat, prf, pre, pfam_fs, and pfam_ls; Pagni et al, 2007) to perform predictions. We ran Motif Scan on the 32 panda-specific proteins.…”

Section: Motif Scan Of Myhitsmentioning

confidence: 99%

“…Data on 21,001 proteins were stored in the Giant Panda Protein Database (GPPD) (http://60.28.101.183/home.html). The functions of these proteins were analyzed using GeneScan (Burge et al, 1997) and subjected to functional classification using SVM-Prot (Cai et al, 2003), motif prediction using MyHits (Pagni et al, 2007), and interacting protein prediction using the Database of Interacting Proteins (DIP) (Xenarios et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

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Functional annotation from the genome sequence of the giant panda

2012

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The giant panda is one of the most critically endangered species due to the fragmentation and loss of its habitat. Studying the functions of proteins in this animal, especially specific trait-related proteins, is therefore necessary to protect the species. In this work, the functions of these proteins were investigated using the genome sequence of the giant panda. Data on 21,001 proteins and their functions were stored in the Giant Panda Protein Database, in which the proteins were divided into two groups: 20,179 proteins whose functions can be predicted by GeneScan formed the known-function group, whereas 822 proteins whose functions cannot be predicted by GeneScan comprised the unknownfunction group. For the known-function group, we further classified the proteins by molecular function, biological process, cellular component, and tissue specificity. For the unknown-function group, we developed a strategy in which the proteins were filtered by crossBlast to identify panda-specific proteins under the assumption that proteins related to the panda-specific traits in the unknown-function group exist. After this filtering procedure, we identified 32 proteins (2 of which are membrane proteins) specific to the giant panda genome as compared against the dog and horse genomes. Based on their amino acid sequences, these 32 proteins were further analyzed by functional classification using SVM-Prot, motif prediction using MyHits, and interacting protein prediction using the Database of Interacting Proteins. Nineteen proteins were predicted to be zinc-binding proteins, thus affecting the activities of nucleic acids. The 32 panda-specific proteins will be further investigated by structural and functional analysis.

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“…More relevant than hydropathy profile, the identification of protein domains and motifs are very useful to predict the protein function compared to other proteins of the same family. In order to comprehend posttranslational modifications, SignalP [34] was used to detect secreted proteins and MotifScan [35] for protein domains prediction. To screen the protein path, MITOPROT and PATS were used to predict if one of this predicted peptides were targeted to mitochondria or apicoplast, respectively.…”

Section: Proteins Characterizationmentioning

confidence: 99%

Bioinformatic tools help molecular characterization of Perkinsus olseni differentially expressed genes

Ascenso

2011

Journal of Integrative Bioinformatics

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In the 80ies, in Southern Europe and in particular in Ria Formosa there was an episode of heavy mortality of the economically relevant clam Ruditapes (R.) decussatus associated with a debilitating disease (Perkinsosis) caused by Perkinsus olseni. This protozoan parasite was poorly known concerning its' differential transcriptome in response to its host, R. decussatus. This laboratory available protozoan system was used to identify parasite genes related to host interaction. Beyond the application of molecular biology technologies and methodologies, only the help of Bioinformatics tools allowed to analyze the results of the study. The strategy started with SSH technique, allowing the identification of parasite up-regulated genes in response to its natural host, then a macroarray was constructed and hybridized to characterize the parasite genes expression when exposed to bivalves hemolymph from permissive host (R. decussatus), resistant host (R. philippinarum) and non permissive bivalve (Donax trunculus) that cohabit in the same or adjacent habitats in Southern Portugal. Genes and respective peptides full molecular characterization depended on several Bioinformatic tools application. Also a new Bioinformatic tool was developed.

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MyHits: improvements to an interactive resource for analyzing protein sequences

Cited by 200 publications

References 27 publications

LRRC8 proteins share a common ancestor with pannexins, and may form hexameric channels involved in cell‐cell communication

LRRC8 proteins share a common ancestor with pannexins, and may form hexameric channels involved in cell‐cell communication

Functional annotation from the genome sequence of the giant panda

Bioinformatic tools help molecular characterization of Perkinsus olseni differentially expressed genes

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