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Overview Array-Check siRNA-Check Primer-Check Peptide-Check Expression-Check Batch Array-Check Batch siRNA-Check Batch Primer-Check Batch Peptide-Check
General ReleaseNotes Database Array-Check siRNA-Check Primer-Check Peptide-Check Batch Array-Check Batch siRNA-Check Batch Primer-Check Batch Peptide-Check Expression-Check

SpliceCenter used to have build 36 chromosomal coordinates for human genes. What changed?

The database was rebuit to pickup the latest genomic, transcript, and microarray probe data. See the Database FAQ page for details. If you would prefer to work with the older data, a shadow copy of the site using the old data is available here.

The exon numbers in SpliceCenter does not match NCBI exon numbering. Why?

The SpliceCenter database build process includes full length transcripts from both RefSeq and GenBank. NCBI exon numbering is done using only RefSeq transcripts which do not always include all the exons found when GenBank transcripts are analyzed. SpliceCenter numbers exons based on evidence from both sources.

We do, however, record NCBI exon numbering. If you examine refseq transcripts (they have accession numbers starting with 'NM_'), you can see the NCBI exon numbering. Use your mouse to point at an exon in a RefSeq transcript. The mouse over box that pops up will show both the SpliceCenter exon number and the NCBI exon number.

How can I get the nucleic or protein sequence for an exon?

Run one of the interactive SpliceCenter utilities (Array-Check, Primer-Check siRNA-Check, or Peptide-Check). In the graphic output, click on an exon. A pop-up window will show the sequence for the transcript. The orange highlight will indicate the sequence of the exon. Toggle the exon dropdown at the top of the page to see the sequence of different exons or toggle to the protein tab to see protein sequence. Note: protein sequence can't be displayed for UTR exons.

What is EVDB and SpliceMiner?

SpliceMiner and EVDB are precursors of SpliceCenter and it's splice variant database. The Genomics and Bioinformatics Group of NCI's Laboratory of Molecular Pharmacology in collaboration with the Bioinformatics Department of George Mason University developed SpliceMiner and EVDB. EVDB is a relational database that contains a comprehensive, non-redundant collection of splice variant data derived from NCBI's Evidence Viewer. SpliceMiner is a web-based tool for querying EVDB and is most often used for high-throughput identification of microarray probe target locations.

SpliceCenter now uses a different technique for building its splice variant database (see here) but EVDB laid the groundwork for the structure and utility of the current splice variant database. SpliceMiner has been retrofit to use the new splice variant database and is still useful for identifying probe target locations for novel microarrays.

What is PrimerMatch?

PrimerMatch is a sequence search engine developed by Nathan Edwards at University of Maryland's Center for Bioinformatics and Computational Biology. It is an open source C++ application that is available from bioinformatics.org. PrimerMatch was selected as the sequence search engine for SpliceCenter utilities because of its ability to quickly find alignments for very short query sequences. BLAT, BLAST, and In-Silico PCR were also evaluated but PrimerMatch was found to provide the best performance for the short siRNA and primer sequences searched by SpliceCenter. Note: We currently only use exact sequence matches. PrimerMatch does a nice job of finding alignments with one or two mismatches. We may add support for this in the future in order to help identify potential off-target and cross-hybridization effects.

The PrimerCheck and siRNA utilities make use of PrimerMatch to identify perfect matches for query sequences within our database of transcript sequences. The transcript database is a FASTA file with transcripts that represent unique splice variants. The compress_seq utility is used to format / index the database for quick searches by PrimerMatch.

Class Exercise

CIT Exercise Data
U133P2_ACP1_EXP.txt
Tiger Team Bioinformatics Group