I am trying to sequence a gene with degenerate primers. The partial sequence which I got is showing 89.5% identity with other sequences (gene of interest) in Blast. When I am doing MSA in NCBI it is showing much more conserved regions comparing to other programs such as mega , clustral w . what could be the reason?
Abhijeet Singh
- Blast and MSA are two different thing.
- Different algorithm/programs for MSA can/usually differ in results, that is nothing surprising. Select one and use it for consistency in your analyses.
1 votes
1 thanks
Anderson Amorim
Dear Swagata Debnath,
Depending on the method you use, it may be based on a stochastic approach, which means that you may have different results running the same alignment different times, even though you use the same tool. Now, imagine using different approaches/tools... It is perfectly normal to have different results.
0 votes
0 thanks
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools
More Swagata Debnath's questions See All
Similar questions and discussions