In this example, 9 residues are correctly aligned over a total alignment length of 10 residues.
Local conservation was avoided by dividing the alignment length of each aligned sequence by its total length.
The parameters for inclusion were a maximum e-value cutoff of 1e-05, a minimum identity of 60%, and a minimum alignment length of 15.
To study specific metabolic pathways, the BA and RJ metagenomes were compared using 1e-05 as the maximum e-value cutoff, with a minimum identity of 60% and a minimum alignment length of 15.
An e-value cut-off of 1×10−10 and a minimum alignment length of 50 basepairs were applied.
Structures displaying more than 95% of identity on a sequence alignment length of more than 90% were ruled out.
A gene was identified as present if it had >50% identity to the query protein and an alignment length of ≥75% of the query length.
First, a blastx search [221] in the NCBI nr.aa database was performed, and all sequences producing an E-value<1E-3 and a minimal alignment length of 33 residues were considered a hit.
For each query sequence, the EST alignments were filtered to include only the ESTs with a sequence identity of greater or equal to 90% and an alignment length of 30 or more residues.
Overall, the average percent identity was approximately 92%, with an average alignment length of 306 bp, and 17,084 contigs (93%) produced one unique alignment to a bovine chromosome (Table S2).
Average percent identity was approximately 92%, with an average alignment length of 384 bp, and 51,087 contigs (91%) produced a unique alignment to a single chromosome (Table S6).
