Question: Word algorithm in BLAST
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gravatar for katherinebridges99
3.9 years ago by
katherinebridges990 wrote:

As for database searching BLAST is used which uses word algorithm and it is heuristic in nature and their 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?

ADD COMMENTlink modified 3.9 years ago by dariober10k • written 3.9 years ago by katherinebridges990
1

serious concerns regarding sensitivity and specificity of word algorithm

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.

ADD REPLYlink written 3.9 years ago by dariober10k

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.

ADD REPLYlink written 3.9 years ago by katherinebridges990

Sure, blast is heuristic. But I was wondering to what extent and under what circumstances this limitation is seriously a concern.

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by dariober10k

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.

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by genomax76k
1

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.

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by Emily_Ensembl20k

As I am a new user that's why committed that mistake but next time I will be careful.

ADD REPLYlink written 3.9 years ago by katherinebridges990
0
gravatar for dariober
3.9 years ago by
dariober10k
WCIP | Glasgow | UK
dariober10k wrote:

If you don't want to trade off performance for sensitivity, you should look for some implementation of the Smith-Waterman algorithm. For example here http://www.biology.wustl.edu/gcg/ssearch.html (never used it myself)

ADD COMMENTlink written 3.9 years ago by dariober10k

Is Smith waterman algorithm also use homology based method for database searching?

ADD REPLYlink written 3.9 years ago by katherinebridges990
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