The structure of the resultant complex contains 8 amino acid residues that span the alignment of Class I as well as Class II JH agonists.
Depending on whether the mapped read is located at the forward or backward strand we have to span the alignment window upstream or downstream.
We constructed the tree from a gapless region of the NA alignment spanning the entire ThiF domain except for the last two bases.
The segment (35%) at the top of group F had a dense contiguous alignment spanning the initial 28% of Mt-2.
This search recovered the GCS2 HMM (based on PDB: 1r8g) as the highly significant best hit (p-value= 10-5), with an alignment spanning the entire length of the GCS2 catalytic domain and matching all key conserved motifs (Fig. 2; see below).
A 146-codon alignment spanning the full-length coding sequence of Atlantic cod β1 globin was obtained with MUSCLE (http://www.ebi.ac.uk/Tools/msa/muscle/) using a total of 13 sequences from six gadiformes, namely Atlantic cod, whiting, haddock, burbot, polar cod (Boreogadus saida) and Arctic cod (Arctogadus glacialis).
A complete list of primers for all exons, a summary of PCR success in each species and Genbank accession numbers are available in additional file 4. Amplicons where all species amplified are available as a multiple alignment spanning the exon and flanking intronic sequences.
Among the genes compared between species above, we were able to root the comparisons by mapping S. franciscanus sequences to 9,258 whole-gene alignments spanning the three species.
Second, specific and degenerate polymerase chain reaction (PCR) primers, able to amplify the intergenic sequence (IGS) between any combination of α- and β-tubulin genes in tandem were designed from sequence alignments spanning the entire Kinetoplastida.
A PSI-BLAST search of flagellin CBO0798 restricted to the Clostridium genus also detected collagen-adhesion proteins with alignments spanning the hypervariable region after three iterations (E = 0.017, ZP_02635881).
Current methods for indel calling assign scores to different types of evidence or counter-evidence for the presence of an indel, such as the number of split read alignments spanning the boundaries of a deletion candidate or reads that map within a putative deletion.
