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Based on sequence-sequence comparison, these programs perform very well for proteins with high sequence identity.
CARD assigns putative antibiotic resistance genes to unannotated microbial genome sequences based on sequence similarity.
Based on sequence similarity, the sequences used here appear to represent the ubiquitously-expressed copy; this copy has been mapped to the Triticeae group 2 homoeologous chromosomes [72].
Further, the example of elongation factor suggests that prediction of secondary structures based on sequence composition and sequence similarity to a 'homologue' should be exercised with caution.
All the remaining sequences were clustered based on sequence similarity using BLASTCLUST program with 90% identity and 80% coverage.
In our approach we match the pyrosequencing reads to full-length, taxonomically classified, reference 16S rRNA sequences, based on sequence similarities deduced by BLAST.
The introduction of gaps in the resulting alignments was minimized by merging sequences based on sequence similarity between subtypes, as reported in phylogenetic studies [5], [67].
In order to minimize problem (3), we employed a sequence alignment based on structure rather than a sequence alignment based on sequence.
A secondary structure based on sequence alignment and sequence covariations was predicted for each element.
Based on sequence homology, 15,633 sequences can be categorized into 48 functional groups.
Based on sequence homology, 13,317 sequences were categorized into 44 functional groups.
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