Identifying Blast hits that are common to two sequences helps to compare remote homologs.
The analysis requires two steps.
Alignment programs perform better when sequences are added that share similarity with the proteins
to be aligned. Using two additional steps one can improve multiple sequence alignments:
- One protein is selected in one, the other in the other protein list.
- For each sequence a BLAST search is performed against a non-redundant set of sequences such as uniref50
- For two sequences the BLAST hits are compared and all common segments presented to the user by pressing the button .
- Choose hits that are similar to either sequence by activating the respective check-boxes.
- Protein objects are created for each activated Blast segment. At this stage overlapping segments with the same sequence ID but different start and end positions are joined.
- Finally a multiple sequence alignment is computed .
Related publications: 11159329 9367767