Bioinformatic tools in analysis ofSequence Alignment:A sequence alignment is method of arranging thesequences of the DNA, RNA, or protein toidentify regions of similarity considering functional, structural, orevolutionary relationships between the sequences. Aligned sequences (nucleotide or amino acid) are represented as rows within a matrix. Gaps areinserted between the residues . It is used for non-biological sequences.Tools:1.
BLASTBasic local alignmentsearch tool.Authors:Altschul SF1, Gish W, Miller W, Myers EW, Lipman DJ. This tool is used for rapid sequence comparison.Itoptimizes the local similarity between the sequences , the MSP (Maximal segmentpair) score.
MSP scores help in analysis and statistical significance ofalignment by use of mathimatical results on the stochastic properties.It helpsin DNA and protein database searches,gene identification searches,motifsearches ,gene identification searches.It is faster simple and efficient tool.2.Clustal OmegaFast, scalablegeneration of high-quality protein multiple sequence alignments using ClustalOmega.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 alignmentusing the progressive alignment heuristic.
It allows the computation of sets ofmany thousands of sequences. It helps in high quality alignments but for numberof sequences it scales badly.It is a new programme which can align proteinssequences quickly and with accurate results.Accuracy on smallest test cases issame as high quality alignments. It performs in terms of concidering time andquality.It has powerful features for adding sequence and exploiting informationand precomputed information in public databases like Pfam.
3.ProtParamProtein Identification and Analysis ToolAuthors:Elisabeth Gasteiger,Christine ,HooglandAlexandre,GattikerS’everine, DuvaudMarc R., WilkinsRon D. AppelAmos ,Bairochs on the ExPASyServerIt performs in the investigation of protein from the2-D gels and mass spectrometry.
It is used for the protein identification andit defines protein as a novel.It predicts the certain protein properties alsoused for the empirical investigation.Swiss prot database for posttranslationalmodification and protein processing. 4.JIGSAW: integration of multiple sources ofevidence for gene prediction.Authors:Allen JE1, Salzberg SL.It is new gene finding system for predicating genestructure from the multiple sources that match the performance of humancurators.
It computes the relative weight of different lines of evidence usingthe dynamic programming. Its performance is superior to ab initio gene findingmethods.It improves gene prediction accuracy and also prediction of completegene structure in human genomic DNA.5.NovoSNpnovoSNP, a novel computational tool for sequencevariation discoveryAuthors:Stefan Weckx, Jurgen Del-Favero1, Rosa Rademakers,Lieve Claes, Marc Cruts, Peter De Jonghe, Christine Van Broeckhoven, and PeterDe RijkIt discovers single nucleotide polymorphism (SNPs)and insertion deletion polymorphism(INDELS ) in a fast way. The first data set comprised 1028 sequence trace filesobtained from diagnostic mutation analysis of SCNIA.The second data setcomprised 9062 sequence.
It is designed for the sequence analysis of clonedtemplates , It offers a user friendly interface for the inspecting geneticvariation 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 multiplesequence 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; Proteinidentification and analysis tools on the ExPASy server.
Springer 571-607. 4.Allen JE, Salzberg SL (2005) JIGSAW: integration ofmultiple sources of evidence for gene prediction. Bioinformatics 21: 3596-3603. 5.Weckx S, Del-Favero J, Rademakers R, Claes L, CrutsM, et al. (2005) novoSNP, a novel computational tool for sequence variationdiscovery. Genome Res 15: 436-442.