I'm looking for something that's more rigorous than BLAST and less rigorous than a global alignment-esque algorithm. Is there a paper out there that compare methods? What's the most popular method?
I'm doing a BLAST search against one protein, and then trying to find closer hits with a better search method. Is there a better way of going about this?
Edit: This question is probably too broad so here are some additional details. I'm interested in transmembrane proteins, so some type of analysis on transmembrane segments of the proteins will be important.