Fasta
Download as PPTX, PDF105 likes65,760 views
FASTA is a bioinformatics tool and biological database that is used to compare amino acid sequences of proteins or nucleotide sequences of DNA. It was first described in 1985 by Lipman and Pearson. FASTA performs fast homology searches to find similarities between a query sequence and sequences in a database. While similar to BLAST, FASTA is faster for sequence comparisons. It works by identifying patches of sequence similarity that may contain gaps. Some key FASTA programs include FASTA, TFASTA, FASTS, and FASTX/Y. FASTA is useful for applications like identification of species, establishing phylogeny, DNA mapping, and understanding protein function.
Fasta
- 2. Bioinformatics Research , development, application of computational tools and approaches for expanding the use of biological , including those to acquire, store, organize, analyze such data.
- 3. Similarity search tools • Computer softwares containing an organized body of sequence of nucleic acid & proteins & designed to update, query & retrieve the data. • They contain amino acid sequences of proteins & nucleotide sequence of nucleic acid. • Find out similarities between the query sequence & data in database are called database similarity search tools.
- 4. FASTA • FASTA package was 1st described as by Lipman & Pearson in 1985. • FASTA is a DNA & protein sequence alignment software. • FASTA is a fast HOMOLOGY search tool. • Similar to BLAST , but this tool will speed up sequence comparison when compared with BLAST. • Hence it is called FASTA.
- 5. Cntd… • FAST-P stands for protein , compare the amino acid sequence of proteins & FAST-N stands for nucleotide alignment , compare the nucleotide sequence of DNA. • It is Bioinformatic tool. • It is biological database. • It compare the amino acid sequence of different proteins or the nucleotide sequence of different DNA.
- 6. FASTA Format • Header line which begins with ‘>’ gives a unique identifier for the sequence. • The gap character ‘-’ is found in locations corresponding to gaps in the sequence. • E.g. >JC2395 NVSDVNLNK--- YIWRTAEKMK---QKIQLLQWYQSHGKT
- 7. Amino acid code Meaning A Alanine B Asparagine C Cysteine D Aspartic acid E Glutamic acid F Phenylalanine G Glycine H Histidine I Isoleucine J Leucine (L) K Lysine L Leucine M Methionine N Asparagine O Pyrrolysine
- 8. Amino acid code Meaning P Proline Q Glutamine R Arginine S Serine T Threosine U Selenocysteine V Valine W Tryptophan Y Tyrosine Z Glutamic acid (E)
- 9. FASTA Programs • FASTA - compares a query protein sequence to a protein library or DNA sequence to a DNA library. • TFASTA – compares a query sequence to a DNA library, after the DNA sequence has been translated in all 6 reading frames. • FASTS – compares a set of ordered peptide fragments, obtained from mass-spectrometry analysis of a protein against a protein database. • FASTX & Y – compares a query DNA sequence to a protein sequence database , translating the DNA sequence in all 6 reading frames.
- 10. salient features of fasta • FASTA find out patches of sequence SIMILARITY between the query and database. • FASTA may contain GAPS. • FASTA is RAPID. • FASTA is working on the basis of FASTA algorithm developed by Fredi and Barton.
- 11. Cntd… • Programs can be run locally or by sending query sequence to the FASTA Email serer. • Program achieve a high level of sensitivity for similarity search at high speed. • FASTA is not guaranteed to find best alignment between the query and database.
- 12. uses of fasta • Identification of species. • Establishing phylogeny. • DNA mapping. • Understanding biochemical functions of protein. • Studying evolution of species. • Identification of mutations. • Calculating molecular weight.
- 13. Cntd… • Studying atomic composition. • Knowing amino acid composition. • Identification of specific function of sequence. • Comparison of DNAs.
- 23. THANKYOU