PBIL

SIM4 - cDNA and Genomic DNA Alignment

BBE contribution to PBIL in Lyon, France

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.
cDNA Sequence:
Origin:
Sequence name (or bank ID/AC):
Strand: Direct Reverse
If user entered, paste raw sequence below:

Genomic Sequence:
Origin:
Sequence name (or bank ID/AC):
Strand: Direct Reverse
If user entered, paste raw sequence below:

SIM4 parameters:
W - word size:
X - value for terminating word extensions:
N - accuracy of sequences:

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 ]
User reference :1208288354

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