Downloaded 1,091 times
Uploaded byShruthi Choudary
Bioinformatics Final Presentation
Bioinformatics analyzes massive amounts of biological data like DNA sequences to uncover hidden biological information. It has many applications like molecular medicine, drug development, and microbial genome analysis. Common bioinformatics tools like BLAST are used to compare query sequences against databases to find similar sequences. BLAST works through a heuristic algorithm that finds short matches between sequences to locate potential homologs in an efficient manner. Other algorithms like Smith-Waterman and FASTA also perform sequence alignment but with different tradeoffs in accuracy and speed.
Bioinformatics Final Presentation
- 1.
- 2. introductionBioinformatics has developedout of the need to understand the code of life, DNA.
- 3. Massive DNA sequencingprojects have evolved and added in the growth of the science of bioinformatics.
- 4. The ultimate goalof bioinformatics is to uncover the wealth of biological information hidden in the mass of sequence, structure, literature and other biological data2
- 5.
- 6.
- 7.
- 8.
- 9.
- 10. What is donein bioinformatics?8
- 11.
- 12.
- 13.
- 14.
- 15.
- 16.
- 17.
- 18.
- 19.
- 20.
- 21.
- 22. Applications of bioinformaticsAntibioticresistance Â
- 23. Forensic analysis ofmicrobes Â
- 24.
- 25.
- 26.
- 27.
- 28.
- 29. Development of Droughtresistance varieties Â
- 30.
- 31. Software and tools12Softwaretools for bioinformatics range from simple command-line tools, to more complex graphical programs and standalone web-services available from various bioinformatics companies or public institutions.
- 32. The computational biologytool best-known among biologists is probably BLAST, an algorithm for determining the similarity of arbitrary sequences against other sequences, possibly from curated databases of protein or DNA sequences.
- 33. BLAST is oneof a number of generally available programs for doing sequence alignment. The NCBI provides a popular web-based implementation that searches their databases. BLASTBasic Local Alignment Search Tool.
- 34. It is analgorithm for comparing biological sequences information, such as amino acid sequence of different proteins or the nucleotides of DNA sequences.
- 35. BLAST is usedto identify library sequences that resembles the query sequences.
- 36. The BLAST programwas designed by Eugene Myers, StephenAltschul, Warren Gish, David J. Lipman and WebbMiller at the NIH and was published in J. Mol. Biol. in 1990.13
- 37. BLAST BLAST isa tool for alignment of sequences.Eg: To identify the unknown gene(query sequences) in the mouse,the scientist will perform a BLAST search of the human genome (library sequences) to see whether the human carrying the similar gene or not. BLAST was originally developed by NCBI( National Center for Biotechnology Information).
- 38. Link: http://www.ncbi.nlm.nih.gov/BLAST/14
- 39. BLASTThe NCBI siteprovides binary files for the following operating systems and platforms. UNIX
- 40.
- 41.
- 42.
- 43. IBM AIX5.115
- 44.
- 45.
- 46.
- 47. Kinds of BLASTNucleotide-nucleotideBLAST (blastn)This program, given a DNA query, returns the most similar DNA sequences from the DNA database that the user specifies.Protein-protein BLAST (blastp)This program, given a protein query, returns the most similar protein sequences from the protein database that the user specifies.Position-Specific Iterative BLAST (PSI-BLAST)This program is used to find distant relatives of a protein. 19
- 48. Kinds of BLASTNucleotide6-frame translation-protein (blastx)This program compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database.Nucleotide 6-frame translation-nucleotide 6-frame translation (tblastx)This program is the slowest of the BLAST family.The purpose of tblastx is to find very distant relationships between nucleotide sequences.Protein-nucleotide 6-frame translation (tblastn)This program compares a protein query against the all six reading frames of a nucleotide sequence database.20
- 49. processBLAST works throughuse of heuristic algorithm.
- 50. Heuristic algorithm ,isan algorithm that is able to produce an acceptable solution to a problem in many practical scenarios.Heuristics are typically used when there is no known method to find an optimal solution ,under the given constraints.21
- 51. process Using aheuristic method ,BLAST finds homologous sequences,not by comparing either sequences in its entirety, but rather by locating short matches between the two sequences. This process of finding initial words is called seeding.
- 52. While attemptingto find homology in sequences, sets of common letters, known as words.22
- 53.
- 54. The sequences containthe following stretch of letters,GLKFA. If aBLASTp was being conducted under default conditions,theword size would be 3 letters.In this case, using the given stretch of letters, the searched words would be GLK, LKF,KFA.
- 55. The heuristic algorithmof BLAST locates all common words between the sequences of interest (query) and the hit sequences(sequences from database).23
- 56. USES OF BLASTBLASTcan be used for several purposes. These include:Identifying Species:With the use of BLAST, you can possibly correctly identify a species and/or find homologous species. This can be useful, for example, when you are working with a DNA sequence from an unknown species.Locating Domains:When working with a protein sequence you can input it into BLAST, to locate known domains within the sequence of interest.24
- 57. USES OF BLASTEstablishingPhylogeny:Using the results received through BLAST, you can create a phylogenetic tree using the BLAST web-page.DNA Mapping:When working with a known species, and looking to sequence a gene at an unknown location, BLAST can compare the chromosomal position of the sequence of interest, to relevant sequences in the database(s).Comparison:When working with genes, BLAST can locate common genes in two related species, and can be used to map annotations from one organism to another.25
- 58. SMITH-WATERMAN ALGORITHMThe Smith-Watermanalgorithm is a well-known algorithm for performing local sequence alignment.
- 59. This method variesfrom the BLAST method in two areas, accuracy and speed.Â
- 60. A better alternativein order to find the best possible results.
- 61. It is moretime consuming.26
- 62. FASTAFASTA is aDNA and protein sequence alignment software package.
- 63. FASTA package containsprograms for protein: protein, DNA:DNA, protein : translated DNA , and ordered or unordered peptide searches.
- 64. Â A major focusof the package is the calculation of accurate similarity statistics, so that biologists can judge whether an alignment is likely to have occurred by chance.27
- 65.