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Bioinformatic tools in analysis of

Sequence Alignment:

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A sequence alignment is method of arranging the
sequences of  the DNA, RNA, or protein to
identify regions of similarity considering functional, structural, or
evolutionary relationships between the sequences. Aligned sequences (
nucleotide or amino acid) are represented as rows within a matrix. Gaps are
inserted between the residues . It is used for non-biological sequences.

Tools:

1.BLAST

Basic local alignment
search tool.

Authors:

Altschul SF1, Gish W, Miller W, Myers EW, Lipman DJ.

 

This tool is used for rapid sequence comparison.It
optimizes the local similarity between the sequences , the MSP (Maximal segment
pair) score.MSP scores help in analysis and statistical significance of
alignment by use of mathimatical results on the stochastic properties.It helps
in DNA and protein database searches,gene identification searches,motif
searches ,gene identification searches.It is faster simple and efficient tool.

2.Clustal Omega

Fast, scalable
generation of high-quality protein multiple sequence alignments using Clustal
Omega.

Authors:

Sievers F1, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG.

 

This tool is used for multiple sequence alignment
using the progressive alignment heuristic.It allows the computation of sets of
many thousands of sequences. It helps in high quality alignments but for number
of sequences it scales badly.It is a new programme which can align proteins
sequences quickly and with accurate results.Accuracy on smallest test cases is
same as high quality alignments. It performs in terms of concidering time and
quality.It has powerful features for adding sequence and exploiting information
and precomputed information in public databases like Pfam.

3.ProtParam

Protein Identification and Analysis Tool

Authors:

Elisabeth Gasteiger,Christine ,HooglandAlexandre,
GattikerS’everine, DuvaudMarc R., WilkinsRon D. AppelAmos ,Bairochs on the ExPASy
Server

It performs in the investigation of protein from the
2-D gels and mass spectrometry. It is used for the protein identification and
it defines protein as a novel.It predicts the certain protein properties also
used for the empirical investigation.Swiss prot database for posttranslational
modification and protein processing.

 

4.JIGSAW: integration of multiple sources of
evidence for gene prediction.

Authors:

Allen JE1, Salzberg SL.

It is new gene finding system for predicating gene
structure from the multiple sources that match the performance of human
curators.It computes the relative weight of different lines of evidence using
the dynamic programming. Its performance is superior to ab initio gene finding
methods.It improves gene prediction accuracy and also prediction of complete
gene structure in human genomic DNA.

5.NovoSNp

novoSNP, a novel computational tool for sequence
variation discovery

Authors:

Stefan Weckx, Jurgen Del-Favero1, Rosa Rademakers,
Lieve Claes, Marc Cruts, Peter De Jonghe, Christine Van Broeckhoven, and Peter
De Rijk

It discovers single nucleotide polymorphism (SNPs)
and  insertion deletion polymorphism
(INDELS ) in a fast way. The first data set comprised 1028 sequence trace files
obtained from diagnostic mutation analysis of SCNIA.The second data set
comprised 9062 sequence.It is designed for the sequence analysis of cloned
templates , It offers a user friendly interface for the inspecting genetic
variation

 

Tool

Description

Reference

BLAST

It
is a search tool, used for DNA or protein sequence search based on identity.           

1
 

Cluster
Omega

Multiple
sequence alignments may be performed using this program.

2
 

ProtParam

Used
to predict the physico-chemical properties of proteins.

3

JIGSAW

To
find genes, and to predict the splicing sites in the selected DNA sequences.           

4

NovoSNP

Used
to find the single nucleotide variation in the DNA sequence.

5

 

 

1.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990)
Basic local alignment search tool. J Mol Biol 215: 403-410.

 

2.

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K,
et al. (2011) Fast, scalable generation of high-quality protein multiple
sequence alignments using Clustal Omega. MolSyst Biol 7: 539.

3.

Gasteiger E, Hoogland C, Gattiker A, Ron D Appel,
Amos Bairoch, et al. (2005) In: The proteomics protocols handbook; Protein
identification and analysis tools on the ExPASy server. Springer 571-607.

 

4.

Allen JE, Salzberg SL (2005) JIGSAW: integration of
multiple sources of evidence for gene prediction. Bioinformatics 21: 3596-3603.

 

5.

Weckx S, Del-Favero J, Rademakers R, Claes L, Cruts
M, et al. (2005) novoSNP, a novel computational tool for sequence variation
discovery. Genome Res 15: 436-442.

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