Baylor BAC-Fisher

The Baylor BAC-Fisher is a tool for finding whole-genome shotgun (WGS) reads useful in the analysis and assembly of localized genomic regions.

Given a set of localized reads or a gene sequence, the BAC-Fisher performs a comparison against a large set of whole-genome shortgun reads for the same organism. Repetitive sequences are discounted automatically; there is need to mask repeats for speed or specificity.

WGS reads with high-quality, non-repetitive overlaps to your sequence are provided to you with several options:

• Overlapping reads: Fasta-formatted sequence and quality files for the WGS reads.

• Contigs: Fasta-formatted contigs from an assembly of your sequences (if genomic) with the WGS reads using phrap. Because phrap does not use mate-pair information and was not originally tuned for this application, many contigs will have problem joins. Small contigs (less than 2000 bases) should be viewed with skepticism.

• Scaffolds: Contigs that have been adjusted, ordered, and oriented based on read pairing, then combined into longer sequences with strings of Ns for the gaps. The quality of sequence is greatly increased over raw contigs, with some loss of questionable sequence.

The initial version of the BAC-Fisher went online in October, 2001. We have many improvements in mind and welcome your feedback.

Upload Sequences to the BAC-Fisher

Please note that any restrictions placed on the original DNA sequencing reads still applies to the collections obtained through the BAC-Fisher.

Credits

The Baylor BAC-Fisher is a service of the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC). Non-Bayler reads have been obtained through the NCBI Trace Archive .