Thanyathon Khetsuphan SIMI/M 5036955

Assignment 6

Select one of your interesting sequences from the database (sequence should be longer than 300 base pair) to do the BLAST search and answer the following questions:
a. What are the different between 6 BLASTs (blastn, blastp, blastx, tblastn, tblastx, PSI-BLAST) ?

b. Use your sequence to do 3 out of 6 BLASTs and discuss "What’s the strength and weakness of BLAST you have selected?"

c. Show us the first hit on each BLAST with their identity or/and similarity scores.d. Summarize the result from 3 BLASTs you select.

What are the different between 6 BLASTs(blastn, blastp, blastx, tblastn, tblastx, PSI-BLAST)?

BLAST (Basic Local Alignment Search Tool) is a utility that is maintained by the National Center for Biotechnology Information (NCBI). BLAST is used to scan a nucleotide or amino acid sequence database for "hits." A BLAST hit contains one or more high-scoring segment pairs (HSPs). A HSP is a pair of sequence fragments, whose alignment is locally maximal, and whose similarity score exceeds some threshold value. NCBI provides an executable, blastall, that is used to perform BLAST searches on BLAST-able data sources, such as GenBank and SWISS-PROT


BLAST search type Description

Nucleotide-nucleotide BLAST ( BLASTn )

A type of BLAST search in which a nucleotide sequence is compared with the contents of a nucleotide sequence database to find sequences with regions homologous to regions of the original sequence.

BLASTp
A type of BLAST search in which an amino acid sequence is compared with the contents of an amino acid sequence database to find sequences with regions homologous to regions of the original sequence.

BLASTx
A type of BLAST search in which a nucleotide sequence is compared with the contents of an amino acid sequence database to find sequences with regions homologous to regions of the original sequence. The query sequence is translated in all six reading frames, and each of the resulting sequences is used to search the sequence database.

tBLASTn
A type of BLAST search in which an amino acid sequence is compared with the contents of a nucleotide sequence database to find sequences with regions homologous to regions of the original sequence. The sequences in the sequence database are translated in all six reading frames, and the resulting sequences are searched for regions homologous to regions of the query sequence.

tBLASTx
A type of BLAST search in which a nucleotide sequence is compared with the contents of a nucleotide sequence database to find sequences with regions homologous to regions of the original sequence. In a tBLASTx search, both the query sequence and the sequence database are translated in all six reading frames, and the resulting sequences are compared to discover homologous regions.

Position-Specific Iterative BLAST (PSI-BLAST)
This program is used to find distant relatives of a protein. First, a list of all closely related proteins is created. These proteins are combined into a general “profile” sequence, which summarises 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 larger group is used to construct another profile, and the process is repeated.By including related proteins in the search, PSI-BLAST is much more sensitive in picking up distant evolutionary relationships than a standard protein-protein BLAST.

What’s the strength and weakness of BLAST you have selected?

blastn can be used to compare a nucleotide sequence with a nucleotide database. However, if the sequence is long and a user needs to find long alignments between very similar sequences, other algorithm of blastn may need to be applied such as MEGABLAST.

blastx can take a nucleotide sequence, translate it, and query it versus a protein database in one step. Disadvantage is a protein database may not be updated and the coding regions of genomic sequences may not be identified properly.

tblastx compares all six reading frames of a query sequence to all six reading frames of a database. It is useful in identifying proteins encoded by single pass read ESTs. But it uses an intensive algorithmic feat that can bring even modern computers to a grinding halt if not used properly


Blast n

Maximum score

Blastx

tblastx

Summarize the result from 3 BLASTs you selectFrom

Balstn, Blastx, tBlastx sequence of calcineurin subunit A were receive showed maximum score in blastn and when use nucleotide sequence of Cna1 to search amino acid , the result show 2027 score maximum with Cryptococcus neoformans var. grubii strain H99 calcineurin A catalytic subunit (CNA1) gene