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Search Tools

There are two types of Search Tools in Bioinformatics. 1) Text Based Search Tools and 2) Sequence Similarity Based Search Tools. 

1) Text Based Search Tools:

a) SRS = Sequence Search and Retrieval Tool. PIR and other protein sequence database searching. 

b) ENTREZ = This is for the nucleotide, GenBank, protein, DDBJ and NCBI searching. It is like a collection of these databases.

c) ExPASy = stands for Expert Protein Analysis System, this is for the SWISS-PROT and other searching.

2) Sequence Similarity Based Search Tools:

a) FASTA: This is a DNA and Protein sequence alignment online software package. This initially observes the word pattern hits, word-word matches of a given length, and matches the potential matches before performing more time consuming search using Smith-Waterman algorithm. The size taken for a work, given by the parameter ktup, controls the sensitivity, and speed of the program. Increasing the ktup value decreases the number of background hits that are found. From the work hits that are returned the program looks for the segments that contain a cluster of nearby hits. It then investigates these segments for a possible match. 
Image result for fasta example
Example of FASTA Format Result

b) BLAST: Basic Local Alignment Search Tool.. There are different types of BLAST. 

BLASTP = matches the protein query against protein database. 

BLASTN = matches the nucleotide query against nucleotide database.

BLASTX = matches 6 frame translated nucleotide query against protein database. 

TBLASTN = matches the protein query against translated (6 frame) nucleotide database. 

TBLASTX = matches the translated nucleotide query against translated nucleotide database. 

PSI-BLAST = Position Specific Iterative BLAST. A list of all closely related proteins is created. These proteins are combined into a general profile sequence, which summarizes significant features present in these sequences. A query against the protein database is then run using this profile, and a larger group of proteins is found. This large group is used to construct another profile. 

PHI-BLAST = Pattern Hit Initiated BLAST.
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