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BLAST searches in NCBI Rat refseq_rna database were carried out using the sequence of the ID stem of BC1 RNA as the query sequence.
The searches within each database were carried out without restrictions on dates or languages.
Similarity searches against public GenBank and in-house database were carried out using the Blast algorithm.
BLAST searches against SwissProt database were carried out for all the proteins (irrespective of their annotation status) of 15 apicomplexan parasites.
Homology searches in database were carried out using the default parameters of the BLAST program on the website http://www.ncbi.nlm.nih.gov blast[ 37].
Searches of the non-redundant (nr) database were carried out at the NCBI using PSI-BLAST [ 56] with default parameters, using different sequences from COG4636 as queries.
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Translation, SRDA and homology search in the converted database were carry out using special functions on VBA language for use in MS Excel (see additional file 2).
A search of the ED database was carried out to identify all patients eligible.
Homology search on the nucleotide and protein database was carried out using the BLAST program with default settings at NCBI (http://www.ncbi.nlm.nih.gov/).nih.gov/
In relation to the GT database, the proposed method performed better than the existing methods, except in comparison with one particular method, in which prior face alignment on the database was carried out, and 0.88% performance difference was reported.
To address this issue, a systematic comparative analysis of amphioxus cDNA database was carried out to identify the homologs or orthoglogs which in the more advanced organisms are involved in lymphocyte-based immunity.
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