SIM4 - cDNA and Genomic DNA Alignment

SIM4 addresses the problem of efficiently aligning a transcribed and spliced DNA sequence (mRNA, EST) with a genomic sequence containing that gene, allowing for introns in the genomic sequence (taking into account consensus splice signals) and a relatively small number of sequencing errors.

This form allows you to perform pairwise local alignments with SIM4 and to visualize them with LalnView. You may use your own sequences or sequences from the EMBL, GenBank or Hovergen data banks. When using sequences from the banks, you may enter either the sequence name or the sequence accession number (for example HUMINS01 or J00265).
If you use SIM4 in any published work, please cite the following reference:
Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M., Miller, W. (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8, 967-974 [ Abstract ]

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