The Web interface to Splign as well as a link to download the standalone application and help documentation are available from the Splign Homepage. Now, in addition to being made available as a standalone tool, Splign is available through a Web interface. The new NCBI spliced-alignment tool, Splign, includes these design features and is used to help annotate higher eukaryotic genomes at NCBI. To produce accurate eukaryotic gene models from transcript alignments, a tool is needed that combines local and global alignment algorithms and accurately tracks splice junctions. Local alignment tools such as BLAST can quickly identify exons but do not include the nonaligning intronic segments in the alignment and lack precision at splice junctions. One of the most reliable ways to identify genes is to align transcript sequences to a genomic sequence. Splign Transcript to Genomic Alignment Tool on the Web Open Mass Spectrometry Search Algorithm (OMSSA)
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