In this case, all the significant alignments were to a hypothetical protein, and the highest scoring alignment was to a protein from Nostoc azollae 0708 (data not shown).
An e-value cut-off of 10-7 was further imposed on the output to obtain the significant alignments within the genome.
However, this interpretation has been challenged by some archaeologists who argue that the midwinter alignment, where the viewer is outside Stonehenge and sees the sun setting in the henge, is the more significant alignment, and the midsummer alignment may be a coincidence due to local topography.
The minimal domain compactness between query and target proteins was calculated between the domain pair with the most significant alignment.
For each BES we recorded the pseudochromosome coordinates of the most significant alignment above a threshold E-value of 10-30.
Thus, if the first significant alignment with a library sequence aligns residues 25 125 at iteration i, later alignment boundaries at iteration i +1 and beyond are ignored; only the initially aligned region (25 125) is used to form the PSSM.
The one exception is TFAM, where the most significant alignment is to a predicted gene product in Tribolium castaneum of the general class of transcription factors which includes TFAM.
To avoid HOEs, PSI-Search always uses the alignment boundary information from the first significant alignment in which a library sequence appears.
Using the blastn algorithm of BLAST+ 2.2.30 [ 36, 37] and the command line options -db nt, -max_target_seqs 1, -outfmt "6 qseqid sseqid staxids sscinames pident length mismatch gapopen value", each DNA and RNA contig was aligned to the NCBI non-redundant nucleotide database and the most significant alignment was returned.
The most significant alignment was then removed, and the second most significant alignment was combined with the remaining query-template alignments in order to generate a multiple sequence alignment using the same algorithm.
