The conservative committee members are aligned to Ms Cunneen's struggle to "completely destroy" Icac, as she herself has put it, yet the audience wants to know more, they want to hear the intercepts, or at least see the transcript.
In our protocol, the BLASTP outputs were first parsed to calculate and store the weight for each query peptide; once these weights were computed the abundance of each KO-family was calculated by adding the frequency-weight of all the peptides aligned to member proteins of the corresponding KO-family.
For each of the five pir subfamilies (bir, cir, yir, kir, vir), all members of a subfamily were globally aligned to all members of the other four subfamilies.
The majority of viral reads (n = 122,487, 55.1%) aligned to members of the Orthomyxoviridae (influenza) family (Table 1).
After removal of self-hits, we scored loci as NB-LRR if they aligned to any member of the extended NB-LRR locus cluster in A. thaliana (see above).
They were also aligned to previous members, and a new profile HMM was constructed for use in the next round of gene prediction.
Sequences were aligned to selected members of the Picornaviridae family by ClustalW and trees were constructed by using the Molecular Evolutionary Genetics Analysis MEGAA) software version 4.0.2 (10 ).
When members of each cluster were aligned to each other or to their closest reference genome, the number of LCBs was reduced, and the overall sequence homology detected between the strains was apparent based on the height of the similarity profile within each LCB.
Ras Baraka, a council member aligned with the mayor, was heard to declare, "Oh my God," while Donald Bradley, the council president, attributed the result in a stage whisper to "the luck of the Irish".
Using samtools (version 0.1.8 [ Li et al. 2009]) to traverse the alignments, we identified all read pairs for which both members align to the M. guttatus reference genome with a mapping quality ≥29, but have abnormal relative alignment positions (pairs not in the expected orientation and/or an insert size ≥1,000 bp).
