Intermediate sequences
Identifying Blast hits that are common to two sequences helps to compare remote homologs.
The analysis requires two steps.
- 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
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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:
- 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
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