Practical Bioinformatics

Practical 1- To Open and Download FASTA File Format from NCBI

FASTA is a DNA and protein sequence alignment software package first described (as FASTP) by David J. Lipman andWilliam R. Pearson in 1985. FASTA is pronounced "fast A", and stands for "FAST-All", because it works with any alphabet, an extension of "FAST-P" (protein) and "FAST-N" (nucleotide) alignment.

In bioinformatics, FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTAsoftware package, but has now become a standard in the field of bioinformatics.

Enter the URL as follows to obtain NCBI home page

http://www.ncbi.nlm.nih.gov/

Type your query word in the blank text box as indicated by the circle eg. Erythropoietin

You will get another page of ENTREZ cross database search in which we can find hits of our query in different databases present in NCBI.

There are 1236 hits in the Nucleotide database so clicking that database or nucleotide we can get nucleotide information of query from that database as indicated by the circle.

You will get a nucleotide database page with different categorized information from which we can select the desired one for eg. Homo sapiens erythropoietin (EPO) mRNA

we will get another screen showing the query information in GenBank File format.

We can convert or view the GenBank file format in FASTA format by clicking the FASTA word (blue color) as indicated by a circle.

After clicking the FASTA we can see another screen containing query information in FASTA file format as shown in left side of this.

The FASTA file obtained in NCBI need not to be download rather it can be copied from the screen above and can be pasted in the notepad or in any other textual program and can be stored under a file name for future use....