An Introduction to Fasta

1. FASTA
Noman Majeed,Roll no: 3022
Submitted to:Inam ul haq
University of Education Okara Campus
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3. Contents
 1 History
 2 Uses
 3 Search method
 4 See also
 5 References
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4. History
 The original FASTA program was designed for
protein sequence similarity searching. FASTA
added the ability to do DNA:DNA searches,
translated protein:DNA searches, and also
provided a more sophisticated shuffling
program for evaluating statistical
significance.[2] There are several programs
in this package that allow the alignment of
protein sequences and DNA sequences.
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5.  The nucleic acid codes supported are
Nucleic Acid Code Meaning Mnemonic
 A A Adenine
 C C Cytosine
 G G Guanine
 T T Thymine
 U U Uracil
 R A or G puRine
 Y C, T or U pYrimidines
 K G, T or U bases which are Ketones
 M A or C bases with aMino groups
 S C or G Strong interaction
 W A, T or U Weak interaction
 B not A (i.e. C, G, T or U) B comes after A
 D not C (i.e. A, G, T or U) D comes after C
 H not G (i.e., A, C, T or U) H comes after G
 V neither T nor U (i.e. A, C or G) V comes after U
 N A C G T U Nucleic acid
 X masked
 - gap of indeterminate length
 The codes supported (24 amino acids and 3 special codes) are:
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7. Uses
 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.
 The current FASTA package contains programs for
protein:protein, DNA:DNA, protein:translated DNA (with
frameshifts), and ordered or unordered peptide searches. Recent
versions of the FASTA package include special translated search
algorithms that correctly handle frameshift errors (which six-frame-
translated searches do not handle very well) when
comparing nucleotide to protein sequence data.
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8. Search method
 FASTA takes a given nucleotide or amino acid sequence and
searches a corresponding sequence database by using local
sequence alignment to find matches of similar database
sequences.
 The FASTA program follows a largely heuristic method which
contributes to the high speed of its execution. It initially observes
the pattern of word hits, word-to-word matches of a given length,
and marks potential matches before performing a more time-consuming
optimized search using a Smith-Waterman type of
algorithm.
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9. Protein
 Protein-protein FASTA Protein-protein Smith-Waterman (ssearch) Global Protein-protein
(Needleman- Wunsch) (ggsearch) Global/Local protein-protein (glsearch) Protein-protein
with unordered peptides (fasts) Protein-protein with mixed peptide sequences (fastf)
Nucleotide
 Nucleotide-Nucleotide (DNA/RNA fasta) Ordered Nucleotides vs Nucleotide (fastm) Un-ordered
Nucleotides vs Nucleotide (fasts) Translated
 Translated DNA (with frameshifts, e.g. ESTs) vs Proteins (fastx/ fasty) Protein vs Translated
DNA (with frameshifts) (tfastx/ tfasty) Peptides vs Translated DNA (tfasts) Statistical
Significance
 Protein vs Protein shuffle (prss) DNA vs DNA shuffle (prss) Translated DNA vs Protein
shuffle (prfx) Local Duplications
 Local Protein alignments (lalign) Plot Protein alignment "dot-plot" (plalign) Local DNA
alignments (lalign) Plot DNA alignment "dot-plot" (plalign)
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10.  Amino Acid Code Meaning
 A Alanine
 B Aspartic acid or Asparagine
 C Cysteine
 D Aspartic acid
 E Glutamic acid
 F Phenylalanine
 G Glycine
 H Histidine
 I Isoleucine
 J Leucine or Isoleucine
 K Lysine
 L Leucine
 M Methionine
 N Asparagine
 O Pyrrolysine
 P Proline
 Q Glutamine
 R Arginine
 S Serine
 T Threonine
 U Selenocysteine
 V Valine
 W Tryptophan
 Y Tyrosine
 Z Glutamic acid or Glutamine
 X any
 * translation stop
 - gap of indeterminate length
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11. See Also
 BLAST
 FASTA format
 Sequence alignment
 Sequence alignment software
 Sequence profiling tool
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13. References
 Jump up ^ Lipman, DJ; Pearson, WR (1985). "Rapid
and sensitive protein similarity searches". Science
227 (4693): 1435–41. doi:10.1126/science.2983426.
PMID 2983426.
 Jump up ^ Pearson, WR; Lipman, DJ (1988).
"Improved tools for biological sequence comparison".
Proceedings of the National Academy of Sciences of
the United States of America 85 (8): 2444–8.
doi:10.1073/pnas.85.8.2444. PMC 280013. PMID
3162770
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