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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

10/26/09 Splice Center Release

  • The splice variant database has been rebuilt with the latest genomic and transcript data available from NCBI. See the Database FAQ for details.
  • Note: Old database is still available here.
  • If you have links to SpliceCenter pages that include chromosomal coordinates (e.g. from previous runs of SpliceCenter batch applicaitons), you will need to rerun these queries to get valid links for the new build or you can modify the links from http://www.tigerteamconsulting.com/SpliceCenter to http://www.tigerteamconsulting.com/SpliceCenter_old.
  • New microarray platforms have been added to Array-Check and Primer-Check. Probes for all microarrays have been realigned to the new build.
  • Microarray build now allows upto 2 mis-matches when aligning probes to transcripts. If there is a mismatch in the alignment, this is indicated in the probe label.
  • Bowtie is now used to align probes to transcripts in Primer-Check and siRNA-Check. Bowtie is faster than the previous search engine especially with mismatch searching.

12/1/08 Splice Center Release

  • The splice variant database has been rebuilt with the latest genomic and transcript data available from NCBI. See the Database FAQ for details.
  • 6 new organisms have been added to SpliceCenter: A. A. thaliana, B. taurus, C. elegans, D. melanogaster, D. rerio, and O. sativa.
  • 16 additional microarray platforms have been added to Array-Check and Primer-Check.
  • Users may now hide or show NMD splice variants in the interactive utilities by selecting 'Show NMD Variants' in the Display Options section.
  • To correct for missing UTR sequence in GenBank transcript sequences, SpliceCenter now predicts the likely extent of variant UTRs by comparison with other transcripts and known poly(A) sites. The predicted UTR sections are drawn as hollow exon segments at the ends of transcripts. The UTR correction has allowed us to more accurately prune duplicate splice variants in the database so that the variants shown represent true splice variation. Predicted UTR segments also provide a more accurate determination of the variants that will / will not be targeted by a given probe. In the following example, The first exon of variants AB028869 through DQ227257 have predicted 5' UTR sections (drawn as hollow boxes at the beginning of exon 1. Also, exon 6 of AB028869 has a predicted 3' UTR section.
  • SpliceCenter now contains mappings of Pfam domains to splice variants. Simply select the 'Show domains?' check box in the Display options section of Array-Check, Primer-Check, siRNA-Check, Peptide-Check or Expression-Check. Colored boxes will then be displayed around the portion of transcripts that code for known protein domains. This feature can be used to identify splice variants that alter the domain composition of the resulting protein. It may also be used to find probes that target coding regions of specific protein domains. When protein domains are displayed, you may click on the domain name in the legend to link to the Pfam site for a description of each domain.


Tiger Team Bioinformatics Group