Experiment 3: To use BLAST tools to search for the organism using sequences.
Introduction:
In bioinformatics, BLAST (basic local alignment search tool) is an algorithm and program for
comparing primary biological sequence information, such as the amino-acid sequences
of proteins or the nucleotides of DNA and/or RNA sequences. A BLAST search enables a
researcher to compare a subject protein or nucleotide sequence (called a query) with a library
or database of sequences, and identify database sequences that resemble the query
sequence above a certain threshold. For example, following the discovery of a previously
unknown gene in the mouse, a scientist will typically perform a BLAST search of the human
genome to see if humans carry a similar gene; BLAST will identify sequences in the human
genome that resemble the mouse gene based on similarity of sequence.
The home page of the BLAST looks, like this. There are options to choose from,
1. Nucleotide BLAST – This is the tool using which you can search nucleotide sequences to
get the most species.
2. BLASTx – This is the tool using which you can get protein sequences from the specific
nucleotide sequence.
3. tBLASTn - This is the tool using which you can get nucleotide sequences from the specific
protein sequence.
4. Protein BLAST - This is the tool using which you can search protein sequences to get the
most species.
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Nucleotide BLAST (NUCLEOTIDE – NUCLEOTIDE)
Step 1: To search the database to get the most accurate results of the particular nucleotide
sequences, just search them here.
Step 2: The results of all the species comes in such a list
There are two different types of results you can watch,
1. By clicking any of the results you will be directed to FASTA file of the result.
2. Graphical Result, which shows the matching using graphical method.
3. Alignment, in this method along with the FASTA file link there is a quick alignment
sequence for faster reference.
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FASTA Files Link
Alignment Results
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Graphical Results
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Protein BLAST (PROTEIN – PROTEIN)
Step 1: To search the database to get the most accurate results of the particular protein
sequences, just search them here.
Step 2: The results of all the species comes in such a list.
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BLASTx (NUCLEOTIDE – PROTEIN)
Step 1: To search the database to get the most accurate results of the particular protein
sequences from nucleotide sequences, just search them here.
Step 2: The results of all the species comes in such a list.
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tBLASTn (PROTEIN - NUCLEOTIDE)
Step 1: To search the database to get the most accurate results of the particular protein
sequences from nucleotide sequences, just search them here.
Step 2: The results of all the species comes in such a list.
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