PBIL

SIM4 - a program to align cDNA and genomic DNA

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 (Florea et al. 1998) 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).

Please site: Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 1998 8:967-74

SIM4 program is available at Webb Miller's Globin Gene Server: http://globin.cse.psu.edu

If you have problems or comments...

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