Sentence examples for blast scans from inspiring English sources

For the BLAST scans, functionally validated KAP-β sequences [9][15][16] and their S. cerevisiae or H. sapiens orthologues (identified as reciprocal best BLAST hits) were used as queries in BLASTp scans of the predicted proteome panel.

Sequence retrieval, BLAST scans, identification, validation and annotation of hits and all associated parsing of text files were carried out in batch mode with scripts written in Perl5 [87], using modules from the BioPerl library [88] and are available from the authors on request.

Where possible, each taxon was assigned, by hand, to a subfamily on the basis of subfamily membership of the BLAST query which first detected the sequence during the initial BLAST scan and three rounds of reciprocal BLAST.

All hits from the first BLAST scan with an e-value less than 10−10 were also collected.

All returned reciprocal best BLAST hits, together with all hits in the initial BLAST scan with e-value <10−10, were collected.

Furthermore, a BLAST scan of phenylalanine-rich proteins within M. tuberculosis revealed that mycobacteria are abundant with proteins rich in phenylalanine (results not shown).

An additional eight hits from the initial BLAST scan with an e-value of less than 0.01, were selected on the basis of (i) being greater than 500 amino acids in length and (ii) fold recognition by FUGUE where sequences were counted as candidates if a KAP-β family member was returned as top hit with ZSCORE greater than 6.

It has been hypothesized that within the phylum Cnidaria, there was an abrupt shift from slow to fast rates of mtDNA evolution in the stem of Medusozoa (Hellberg 2006), which may be connected to the loss of an msh1 gene in medusozoans: This gene is absent from all available medusozoan mtDNAs and a blast scan of 6 Giga bases of A. moseri nuclear DNA data failed to uncover a nuclear copy of msh1.

For sequences retrieved with e-value of 0.0001 or less in any of the PSI-BLAST scans, the sequence segment giving the lowest e-value was identified.

For the PSI-BLAST scans, Pfam [46] domains IBN_N (PF03810, Importin-β N-terminal) and Xpo1 (PF08389, Exportin 1-like protein), which are specific to several KAP-β family members, were used as query sequences in blastpgp (PSI-BLAST) [45]) searches.

The input of each PSI-BLAST scan included the pfam domain alignment (ie, 'jump-start' from MSA mode) and the maximum number of rounds was set to three.