February 08, 2002 (Friday)
New search and filter options were added to the query tool which seachs for homology among pig ESTs and human UniGene sequences.
Recent Web Log Statistics revealed that the pig EST web site and the pig EST database have received a considerable number of visits from users worldwide.
Feb. 6, 2002 Web Log Summary is added to the pig EST web page. It presents monthly reports and the up-to-date report since the commencement of the web site reconstruction (Dec 2000). The current monthly reprot is updated daily.
A java based in-silico mapping tool is developed and under testing.
A total of 98,988 pig EST sequences were analyzed to search homologies among pig EST sequences and human genes using BLAST alignment against 97,1000 human UniGene sequences. The similarity among the EST sequences and pig gene sequences was also determined by BLAST alignment against 3,331 pig gene sequences. It revealed that
The dbEST IDs and Genbank accession numbers of 14,602 pig ESTs have been obtained. This
resource is being integrated into the pig EST database. The dbEST ID and Genbank accession nu
mber is being used to link the pig EST database to the NCBI databases for additional information.
A collection of 10,000 public pig ESTs from 14 cDNA libraries derived from whole embryo, term placenta, anterior pituitary, hypothalamus and ovary were utilized in this project.
Nucleotide similarities between pig ESTs and human genes were determined by BLAST alignment against human Unigene sequences.
Consequently, a number of putative human orthologs of pig ESTs were identified. The map locations of the pig ESTs were inferred according to cytogenetic maps of their putative human orthologs.
Information on human LociLink, Sequence Tagged Sites (Unists),and the hybrid (RH) map location (GeneMap'99) were used to identify the order of the putative human orthologs of pig ESTs on human chromosomes. The pig-on-human comparative maps and homology between pig and human were then used to predict pig EST assignments on pig chromosomes.
Based on the EST analysis, a pig EST relational database has been created using the Ingres® II Database Management System (Computer Associates®).
This database is comprised of a number of tables covering the EST profile (identity, library, sequence, etc), alignment similarity (human ortholog official symbol and description, identity, overlap), cytogenetic map, linkage map, and RH map of the human orthologs. Visualized presentation and interactive query interfaces are being developed for public access to the EST database
A number of PERL scripts were written for parsing the BLAST output, integrating it with human gene maps and pig-human comparative map information. Database administration and web query tools were developed using the DBI PERL module. [an error occurred while processing this directive]