PSI-BLAST is based on BLAST which has been published by Altschul et al.
For the experimental results, [Q.sub.3], SOV94, SOV99, and recall of our method are higher than those of the SVMpsi method based on the PSI-BLAST profiles as well as the SVMfreq method based on the frequency profiles with multiple sequence alignment for the CB513 data set.
in the National Center for Biotechnology Information (NCBI), we searched the sequences based on the query (UniprotKB ID: Q9H3M7) with which we generated the five templates for Thioredoxin which are shown in (Figure 1).
Also known as HER2/Neu ERK Extracellular signal-regulated Kinases Ile amino acid isoleucine MEK Mitogen-activated protein kinase kinase NCBI National Center for Biotechnology Information PSI-BLAST
Position-Specific Iterative BLAST Val amino acid Valine Table 2.
La anotacion funcional de las secuencias COS predichas en Ipomoea batatas se realizo usando localmente el programa BLASTX (Altschul et al., 1997), y de modo online mediante los programas INTERPROSCAN (Quevillon et al., 2005) localizado en: http://www.ebi.ac.uk/lnterProScan/, y PSI-BLAST (Altschul & Koonin, 1998) localizado en: http://www.ncbi.nlm.nih.gov/BLAST/.
Iterated profile searches with PSI-BLAST -a tool for discovery in protein databases.
Contig-5199 Proteina regulatoria de la adhesion PSI-BLAST celular ARM_1, EB30-H4.e Fenilalanina t-RNA sintetasa BLASTX EB32-D8.e Inhibidor de cisteina proteasas BLASTX Contig-5112 Proteina de union a Acil-CoA (ACBP) BLASTX EB30-E1.e Proteina expresada No anotada EB28-C1.e Glutation S transferasa microsomal BLASTX EB31-G3.b Ubiquitina BLASTX Contig-5041 Proteina de union a DNA BLASTX Contig-5172 Dehalogenasa BLASTX EB28-H3.e Cytocromo c oxidasa INTERPRO EB29-B3.e Proteina expresada No anotada Tabla 4.
Likewise, PSI-BLAST searches failed to identify MBP homologs.
Extending the analyses to the Ciona intestinalis EST database and with PSI-BLAST both failed to identify [P.sub.0] homologs in sea squirt.
An additional candidate (ci0100150877--DM-3) was obtained from the PSI-BLAST search (Table 2).
The original PSI-BLAST results were used for the sequences where no rules could be induced.
We compared the area under the ROC (AUROC) for homology induction and PSI-BLAST. The AUROC value for homology induction was 0.65, and the AUROC for PSI-BLAST 0.61.