A Perl script was used to retrieve KEGG Orthology (KO) information from blast result and then established pathway associations between unigenes and database.
A Perl script was used to retrieve KO (KEGG Ontology) information from the Blast result and establish pathway associations between UniGene and the database.
A Perl script was used to retrieve KO (KEGG Ontology) information from the BLAST search result so that pathway associations between unigenes and the database could be established (Additional file 12).
Blastx alignment (E value < 0.00001) between unigenes and protein databases (NCBI non-redundant protein database, Swiss-Prot, KEGG and COG) was successively performed.
BLASTX alignment (e-value <0.00001) between unigenes and protein databases including non-redundant protein database (NR) (ftp://ftp.ncbi.nih.gov/blast/db/nr), Swiss-Prot (http://www.ebi.ac.uk/swissprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp/kegg/), and clusters of orthologous groups (COG) (http://www.ncbi.nlm.nih.gov/COG/) were performed.
In order to decide sequence direction of unigenes, a BlastX alignment (e value < 10−5) between unigenes and protein databases like nr (non redundant nucleotide database, NCBI), Swiss-Prot, KEGG (Kyoto Encyclopedia of Genes and Genomes) and COG (Clusters of Orthologous Groups) was performed and the best alignment result was chosen.
In the final step, BLASTx alignment (E-value<0.00001) between unigenes and protein databases like Nr, Swiss-Prot, KEGG and COG was performed.
Then, a BLASTx alignment (E-value < 0.00001) between unigenes and protein databases, such as NR, Swiss-Prot, KEGG and COG, was performed, and the best alignment results were used to determine the sequence direction of the unigenes.
For further analysis, we used BLASTX (E-value < 10−5) to compare between unigenes and protein databases such as NCBI nr, Swiss-Prot, KEGG, and COG, and the best aligning results were used to decide the sequence direction of the unigenes.
Finally, BLASTx alignment (E < 10 5) between unigenes and protein databases such as non-redundant protein (Nr), Nucleotide (Nt), Swiss-Prot and KEGG, then COG was performed, and the best aligning results used to determine sequence direction of unigenes.
