After alignment to any CDs, the query sequence forms part of a multiple alignment, represented with a single residue count in each column.
In this scenario, the query consists of a base pairing probability matrix, which can be derived either from a single sequence or from a multiple alignment representing a set of known representatives.
Then, based on the alignment of the ESTs within the cluster, another Bayesian calculation generates the probability that a variant at a given location of a multiple alignment represents a true polymorphism as opposed to a sequencing error.
The second letter, 'm/u/N', indicates the alignment to the reference genome sequence, 'm' represents multiple alignments, 'u' represents unique alignment and 'N' represents no alignment results.
These alignments were used to form multiple sequence alignments representing each PUT sequence and were subsequently examined for polymorphic positions.
A similar approach was carried out where each of Arabidopsis and rice genome sequences was scanned against protein family profiles obtained from the NCBI National Centre for Biotechnology Informationn) conserved domain database (NCBI-CDD[ 18]), a compilation of multiple sequence alignments representing protein domains.
Curated multiple sequence alignments representing WRD-A (Additional file 7, 19 sequences) and WRD-B (Additional file 8, 32 sequences) subdomains were then converted into Stockholm format at http://myhits.isb-sib.ch/cgi-bin/reformat and used as input for HMMER3 searches (default parameters).
Then, for each component, it captures the slight variants of the genomes of subspecies from the same species by multiple alignments and represents the genome of one species, using a consensus sequence.
The five Xl-PSIDs with multiple cDNA clone alignments represent hemoglobin, gamma G (hbg2-a); ferritin light chain (ftl); ribosomal protein S12 (rps12an; an unknown sequence; and cytochrome c oxidase subunit Va (cox5a).
We also hand-curated a multiple sequence alignment representing the complete WRD consisting of one WRD-A and two WRD-B subdomains (Additional file 9).
