Translated sequences (six reading frames) were searched using BLASTX against the non-redundant NCBI protein database (nr) as well as the Swiss-Prot [ 48] division of the same database.
Considering this new division of the Ekofisk database, we design the MLP (tuning of its parameters), as done for the original case of study, and we test it.
In order to test this, we gathered the protein sequences of the orthologs of ERG2, 6, 24, 25, 26 and 28 listed in the HomoloGene division of the NCBI database and estimated their pI (http://www.expasy.ch/tools/pi_tool.html).html
These sequences were deposited in a division of the GenBank Database to the Expressed Sequence Tags (dbEST).
The sequences reported in this paper have also been submitted into dbEST division of the public database GenBank: E. coloratus [GenBank: GR947900- GR948969], E. c. sochureki [GenBank: GR948970- GR950126] and E. p. leakeyi [GenBank: GR950127- GR951204].
We also were able to find a number of orthologs of the newly identified ABHs in other fully sequenced metazoan genomes (Table 1) and in the EST division of the GenBank database (data not shown, links between the individual genes/contigs/transcripts are available via the Ensembl website using the gene identifiers provided in Table 1).
Using the sequence of the C. eugametos chloroplast Ceu ClpP intein as a query in a TBLASTN search of the whole genome shotgun (WGS) sequence division of the GenBank database we detected a high quality match in P. nodorum sequence AAGI01000064 (E = 3 × 10-6; bases 49105 50471).
Next, the division of the available databases of H s measurements is discussed.
The following resources are available at BeeBase [ 121], a division of the Hymenoptera Genome Database [ 88]: genome browsers with gene annotations and supporting evidence alignments; BLAST databases with the Amel_4.5 scaffold assembly, OGSv3.2, all input gene prediction sets and transcript contig assemblies; and a data download page with fasta sequence files and gff for annotations.
Running on a dual-processor Intel Pentium 4 CPU 3.00 GHz with 4 Gb of RAM, the programme takes an average of 0.7 s to annotate each sequence (mean length = 400 amino acids) against a division of the Swiss-Prot database (∼45 000 sequences), using the three modules.
