GeneWise - Dna Block Aligner

Basic Query

Dna Block Aligner (DBA) aligns two sequences under the assumption that the sequences share a number of colinear blocks of conservation separated by potentially large and varied lengths of DNA in the two sequences. The aim was that this was a very sensible thing to do with syntenous regions of non coding DNA between say mouse and human, for example, the upstream regions of a gene from mouse and human, or the conserved intron of a human - chicken gene. The conserved blocks may be regions important for regulation of the gene.

The conserved blocks may have one or two gaps in them.

The final model is a probabilistic finite state machine (or pair-HMM) which aligns the two sequences. Each block is can choose one of 4 different parameter sets, roughly being conservation at 65,75,85 or 95 percent identity. Linear gaps (gaps where the gap open is the same as the extension) have been modeled in the blocks at a fixed probability 0.05 and each block is expected around 1% of the DNA sequence.

The form works by submitting your two sequences in the windows below (you can use the file upload feature if you like) and then clicking submit. An ASCII output of the alignment is returned to you.