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Jit created a page Some useful Bioinformatics links- Abhimanyu Singh commented on the blog Important Journals, Blogs and Forums for Bioinformaticians
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- BioStar 674 days ago
Following steps need to followed while doing any homology search.
BLAST (Basic Local Alignment Search Tool) is a widely used program for searching a database of sequences to find those that match a query sequence. Here are the general steps for performing a BLAST search:
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Choose the BLAST program: BLAST has several different programs that are tailored to different types of queries and databases. The most common programs are blastp, blastn, blastx, tblastn, and tblastx. Choose the program that is appropriate for your query and database.
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Prepare the query sequence: The query sequence should be in a FASTA format and can be entered directly into the BLAST website or saved as a file for local searches.
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Choose the database: BLAST searches can be performed against many different databases, including the NCBI GenBank, RefSeq, and non-redundant databases. Choose the database that is most appropriate for your search.
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Set the parameters: BLAST has many different parameters that can be adjusted to customize the search. The most important parameters include the e-value threshold, the word size, and the gap penalties.
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Perform the search: Once the query sequence and parameters have been set, the BLAST search can be run. This can be done online using the NCBI BLAST website or locally using the command-line interface.
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Interpret the results: After the search is complete, the results can be viewed and downloaded. The results include information about the sequences that matched the query sequence, including the alignment score, identity, and e-value.
Overall, BLAST is a powerful tool for searching sequence databases and can be used for many different types of analyses, including gene annotation, functional annotation, and comparative genomics.
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- LEGE 672 days ago
BLAST compares a query sequence to a database of known sequences and identifies the most similar matches. This is useful for identifying the function of a newly discovered gene or for understanding the evolutionary relationships between different organisms.
BLAST works by breaking down the query sequence into smaller segments, called "words," and searching for matches to those words in the database. It then expands the matches to identify longer regions of similarity, called "alignments," and calculates a score for each alignment that reflects its degree of similarity.
BLAST is widely used in biological research because it is fast, efficient, and easy to use. It has helped researchers make many important discoveries, including identifying new genes and understanding the genetic basis of diseases.
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