Entering edit mode
8.7 years ago
As for database searching BLAST is used which uses word algorithm and it is heuristic in nature and there are serious concerns regarding sensitivity and specificity of word algorithm. Is their any other mechanism or algorithm for database searching which can increase the efficiency of database searching and we can get reliable results?
Do you have a reference for this with the respect to BLAST results?
About your question, it depends on the size of your query and database and your aim. If not too large, even an exhaustive, brute force search could do.
Essential Bioinformatics book chapter four "heuristic methods are limited in sensitivity and are not guaranteed to find optimal alignment" as word algorithm is heuristic in nature so I said that their will be concerns also regarding its sensitivity so actually I want to know that is their any other methods available that are more sensitive then word algorithm for database searching.
Sure, blast is heuristic. But I was wondering to what extent and under what circumstances this limitation is seriously a concern.
For all practical purposes blast should give you "reliable" results. It is possible that the default alignment generated by BLAST may not be optimal but that is something you would edit manually, when you finally do a multiple sequence alignment, if you were doing a homology search/building a phylogenetic tree.
Please use more specific titles and tags when putting questions in BioStars. The tag you have chosen ("bioinformatics" - literally the entire topic of this forum) makes your question impossible to search for, and your title ("Database searching") makes it impossible to determine if it is of any interest. I have added "blast" as a tag and changed your title to reflect the content of your question. In future, please create meaningful titles and tags yourself.
As I am a new user that's why committed that mistake but next time I will be careful.