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The mining of toxin-like polypeptides from EST database by single residue distribution analysis.

Kozlov S, Grishin E - BMC Genomics (2011)

Bottom Line: The adequacy of motifs for mining toxin-like sequences was confirmed by their ability to identify 100% toxin-like anemone polypeptides in the reference polypeptide database.Analysis of 39939 ESTs of sea anemone Anemonia viridis resulted in identification of five protein precursors of earlier described toxins, discovery of 43 novel polypeptide toxins, and prediction of 39 putative polypeptide toxin sequences.In addition, two precursors of novel peptides presumably displaying neuronal function were disclosed.

View Article: PubMed Central - HTML - PubMed

Affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia.

ABSTRACT

Background: Novel high throughput sequencing technologies require permanent development of bioinformatics data processing methods. Among them, rapid and reliable identification of encoded proteins plays a pivotal role. To search for particular protein families, the amino acid sequence motifs suitable for selective screening of nucleotide sequence databases may be used. In this work, we suggest a novel method for simplified representation of protein amino acid sequences named Single Residue Distribution Analysis, which is applicable both for homology search and database screening.

Results: Using the procedure developed, a search for amino acid sequence motifs in sea anemone polypeptides was performed, and 14 different motifs with broad and low specificity were discriminated. The adequacy of motifs for mining toxin-like sequences was confirmed by their ability to identify 100% toxin-like anemone polypeptides in the reference polypeptide database. The employment of novel motifs for the search of polypeptide toxins in Anemonia viridis EST dataset allowed us to identify 89 putative toxin precursors. The translated and modified ESTs were scanned using a special algorithm. In addition to direct comparison with the motifs developed, the putative signal peptides were predicted and homology with known structures was examined.

Conclusions: The suggested method may be used to retrieve structures of interest from the EST databases using simple amino acid sequence motifs as templates. The efficiency of the procedure for directed search of polypeptides is higher than that of most currently used methods. Analysis of 39939 ESTs of sea anemone Anemonia viridis resulted in identification of five protein precursors of earlier described toxins, discovery of 43 novel polypeptide toxins, and prediction of 39 putative polypeptide toxin sequences. In addition, two precursors of novel peptides presumably displaying neuronal function were disclosed.

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Pattern search limitation. Six translated frame should be screened by selected motifs. Sequence fragments between translations stops, in which hit search allowed, are boxed. Identity search for fragment to pattern is permitted inside single fragment and restricted by a multiple fragments implication.
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Figure 3: Pattern search limitation. Six translated frame should be screened by selected motifs. Sequence fragments between translations stops, in which hit search allowed, are boxed. Identity search for fragment to pattern is permitted inside single fragment and restricted by a multiple fragments implication.

Mentions: To decrease the number of false positive results during converted database screening, the limitations on the search parameters were imposed. The identity to the screening line was searched only on long fragments started from the beginning or, after any termination symbols and ending by another termination symbol (see Figure 3). If the fragment did not end by the termination symbol, it was rejected as partially identified. The screening analysis was performed on each fragment separately thus a pattern motif must to match completely in the extent of analyzed fragment. This approach considerably decreased the number of false positive results, since it excluded hits with sequences containing internal stop codons (an example of false hit is given in Figure 3).


The mining of toxin-like polypeptides from EST database by single residue distribution analysis.

Kozlov S, Grishin E - BMC Genomics (2011)

Pattern search limitation. Six translated frame should be screened by selected motifs. Sequence fragments between translations stops, in which hit search allowed, are boxed. Identity search for fragment to pattern is permitted inside single fragment and restricted by a multiple fragments implication.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3040730&req=5

Figure 3: Pattern search limitation. Six translated frame should be screened by selected motifs. Sequence fragments between translations stops, in which hit search allowed, are boxed. Identity search for fragment to pattern is permitted inside single fragment and restricted by a multiple fragments implication.
Mentions: To decrease the number of false positive results during converted database screening, the limitations on the search parameters were imposed. The identity to the screening line was searched only on long fragments started from the beginning or, after any termination symbols and ending by another termination symbol (see Figure 3). If the fragment did not end by the termination symbol, it was rejected as partially identified. The screening analysis was performed on each fragment separately thus a pattern motif must to match completely in the extent of analyzed fragment. This approach considerably decreased the number of false positive results, since it excluded hits with sequences containing internal stop codons (an example of false hit is given in Figure 3).

Bottom Line: The adequacy of motifs for mining toxin-like sequences was confirmed by their ability to identify 100% toxin-like anemone polypeptides in the reference polypeptide database.Analysis of 39939 ESTs of sea anemone Anemonia viridis resulted in identification of five protein precursors of earlier described toxins, discovery of 43 novel polypeptide toxins, and prediction of 39 putative polypeptide toxin sequences.In addition, two precursors of novel peptides presumably displaying neuronal function were disclosed.

View Article: PubMed Central - HTML - PubMed

Affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia.

ABSTRACT

Background: Novel high throughput sequencing technologies require permanent development of bioinformatics data processing methods. Among them, rapid and reliable identification of encoded proteins plays a pivotal role. To search for particular protein families, the amino acid sequence motifs suitable for selective screening of nucleotide sequence databases may be used. In this work, we suggest a novel method for simplified representation of protein amino acid sequences named Single Residue Distribution Analysis, which is applicable both for homology search and database screening.

Results: Using the procedure developed, a search for amino acid sequence motifs in sea anemone polypeptides was performed, and 14 different motifs with broad and low specificity were discriminated. The adequacy of motifs for mining toxin-like sequences was confirmed by their ability to identify 100% toxin-like anemone polypeptides in the reference polypeptide database. The employment of novel motifs for the search of polypeptide toxins in Anemonia viridis EST dataset allowed us to identify 89 putative toxin precursors. The translated and modified ESTs were scanned using a special algorithm. In addition to direct comparison with the motifs developed, the putative signal peptides were predicted and homology with known structures was examined.

Conclusions: The suggested method may be used to retrieve structures of interest from the EST databases using simple amino acid sequence motifs as templates. The efficiency of the procedure for directed search of polypeptides is higher than that of most currently used methods. Analysis of 39939 ESTs of sea anemone Anemonia viridis resulted in identification of five protein precursors of earlier described toxins, discovery of 43 novel polypeptide toxins, and prediction of 39 putative polypeptide toxin sequences. In addition, two precursors of novel peptides presumably displaying neuronal function were disclosed.

Show MeSH