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This may be because PSI-BLAST utilizes multiple sequence profiles that enhance the recognition of the sequence-function relationship.
Finally, sequence data for one of the 3 HERV-H coding env genes studied (i.e. envH2) yielded multiple sequence profiles (possibly due to the parasitic amplification of another member of the HERV-H family) and could not be analyzed further.
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We carried out multiple sequence profile searches with different starting points of carboxylate-amine/ammonia ligase superfamily to identify additional members.
To further investigate the role of these proteins across distinct SOS-associated mutagenic processes we initiated multiple sequence profile and hidden Markov searches with the PSI-BLAST and JACKHMMER programs respectively and obtained a comprehensive collection of its members (Additional file 1).
Importantly, we found that there is a significant variation among multiple sequencing profiles of input DNA libraries and that this variation most likely arises from both differences in experimental condition and sequencing depth.
Multiple sequence alignment profiles were created using the Muscle sequence comparison tool from Embl-EBI (Edgar, 2004a, 2004b).
The sensitivity of these methods derives from comparing a multiple sequence alignment profile built from query homologs to similarly derived profiles of existing structures.
These profiles were based on multiple sequence alignments and profile-hidden Markov models from the 'Pfam' protein family database [13].
Homology-based gene predictions were then performed for each region using multiple approaches with sequence profiles or individual protein sequences.
It has been used in many bioinformatics areas such as motif identification [ 5, 6], gene structure prediction [ 7], multiple sequence alignment [ 1- 4], profile-profile alignment [ 8, 9], protein sequence database search [ 1, 3], protein fold recognition [ 1, 3, 9], and protein and gene family modeling (profile HMM) [ 1- 4].
AntiFam is a freely available collection of multiple sequence alignments and profile HMMs.
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