GenomicVariation_11-22
... by conservation level. -- Uses BLAT local alignment tool to find seeds of high sequence similarity, then these seeds are used for global single- or multiple-genome alignment ...
... by conservation level. -- Uses BLAT local alignment tool to find seeds of high sequence similarity, then these seeds are used for global single- or multiple-genome alignment ...
Investigation #3
... DNA sequence of several genes was obtained. Use this to place the organism. ...
... DNA sequence of several genes was obtained. Use this to place the organism. ...
Slide 1
... In biological sequences, a gap is often longer than 1. For example, the insertion of a new functioning domain. A long gap may be penalized too much by the previous methods. - assign two different penalties: gap initiation penalty. gap extension penalty. Now at every position, 3 values, instead of 1, ...
... In biological sequences, a gap is often longer than 1. For example, the insertion of a new functioning domain. A long gap may be penalized too much by the previous methods. - assign two different penalties: gap initiation penalty. gap extension penalty. Now at every position, 3 values, instead of 1, ...
Sequence alignment
... 2. Now think of appropriate keywords and use them to search in a. GQuery (http://www.ncbi.nlm.nih.gov/gquery) b. EMBL-EBI (http://www.ebi.ac.uk/services) 3. Observe the number of entries found in different databases. a. What keywords did you use? b. How many protein sequences did you find in each of ...
... 2. Now think of appropriate keywords and use them to search in a. GQuery (http://www.ncbi.nlm.nih.gov/gquery) b. EMBL-EBI (http://www.ebi.ac.uk/services) 3. Observe the number of entries found in different databases. a. What keywords did you use? b. How many protein sequences did you find in each of ...
Document
... "Where the homology is a result of gene duplication so that both copies have descended side by side during the history of an organism, (for example, alpha and beta hemoglobin) the genes should be called paralogous (para=in parallel). Where the homology is the result of speciation so that the history ...
... "Where the homology is a result of gene duplication so that both copies have descended side by side during the history of an organism, (for example, alpha and beta hemoglobin) the genes should be called paralogous (para=in parallel). Where the homology is the result of speciation so that the history ...
Advantages/disadvantages of BLAST vs FASTA
... b. In what sense is BLAST better than the Smith-Waterman (local alignment) DP algorithm? ...
... b. In what sense is BLAST better than the Smith-Waterman (local alignment) DP algorithm? ...
Derivation and refinement of global sequence motifs for the integral
... Michael Sadowski, J. Howard Parish and David R. Westhead Previously, an alignment algorithm for matching flexible, sequence-length motifs (‘signatures’) to protein sequences has been described and a method of deriving these motifs using contact information derived from the crystal structures of vari ...
... Michael Sadowski, J. Howard Parish and David R. Westhead Previously, an alignment algorithm for matching flexible, sequence-length motifs (‘signatures’) to protein sequences has been described and a method of deriving these motifs using contact information derived from the crystal structures of vari ...
amino acid substitution scores
... BLOSUM Matrices. Steve and Jorja Henikoff took an alternative approach to determining a family of scoring matrices. They used their BLOCKS database, which contains ungapped multiple alignments, called blocks, of core regions from hundreds of protein families. (The name BLOSUM stands for BLOcks SUbst ...
... BLOSUM Matrices. Steve and Jorja Henikoff took an alternative approach to determining a family of scoring matrices. They used their BLOCKS database, which contains ungapped multiple alignments, called blocks, of core regions from hundreds of protein families. (The name BLOSUM stands for BLOcks SUbst ...
Amino Acid Substitution Scores
... the PAM30, PAM70, BLOSUM80, BLOSUM62 and BLOSUM45 matrices that are available on NCBI’s blastp server. Such scores are appropriate for comparing two sequences about which we have no other information (as opposed to position specific scores tailored for a particular protein family). Thus, we seek a 2 ...
... the PAM30, PAM70, BLOSUM80, BLOSUM62 and BLOSUM45 matrices that are available on NCBI’s blastp server. Such scores are appropriate for comparing two sequences about which we have no other information (as opposed to position specific scores tailored for a particular protein family). Thus, we seek a 2 ...
Introductory Biological Sequence Analysis Through Spreadsheets
... R.F. Murphy at CMU has developed a set of worksheets for sequence analysis November 18, 2000 ...
... R.F. Murphy at CMU has developed a set of worksheets for sequence analysis November 18, 2000 ...
m12-comparative_genomics
... Organize a collection of modern-day sequences according to their evolutionary history Distance-based methods operate on a table of pairwise distances between sequences o UPGMA: ~agglomerative clustering; naïve method for tree-building; assumes a molecular clock (all branches changing at the same ...
... Organize a collection of modern-day sequences according to their evolutionary history Distance-based methods operate on a table of pairwise distances between sequences o UPGMA: ~agglomerative clustering; naïve method for tree-building; assumes a molecular clock (all branches changing at the same ...
CIPRES.2006.algorthms_sr
... • Gene Order. Can reconstruct phylogenies from gene order data with logarithmic number of genes. (Adkins et al.) • Supertree Methods. Reconstructing trees from Triplets, Quartets. (Snir et al.) Combining above into supertree method. • Reticulate Evolution: (Karp, Riesenfeld). Produces Galled trees f ...
... • Gene Order. Can reconstruct phylogenies from gene order data with logarithmic number of genes. (Adkins et al.) • Supertree Methods. Reconstructing trees from Triplets, Quartets. (Snir et al.) Combining above into supertree method. • Reticulate Evolution: (Karp, Riesenfeld). Produces Galled trees f ...
word - Mr Idea Hamster
... proteins booboos, protein functions, amino acid sequences, and nucleotide sequences. 5. Study an amalgamation of disease/gene/protein using the NCBI website. 6. Perform basic bioinformatics procedures regarding—homologues and orthologs, SNPs, cladograms, e-PCR, 3D protein models, and gene expression ...
... proteins booboos, protein functions, amino acid sequences, and nucleotide sequences. 5. Study an amalgamation of disease/gene/protein using the NCBI website. 6. Perform basic bioinformatics procedures regarding—homologues and orthologs, SNPs, cladograms, e-PCR, 3D protein models, and gene expression ...
Slide 1
... •Multiple alignment is an extension of pairwise alignment where multiple sequences are aligned •This alignment provides insights not possible in pairwise alignments, such as •Conserved sequence patterns •Conserved and functionally critical amino acid residues •Prerequisite for phylogenetic analyses ...
... •Multiple alignment is an extension of pairwise alignment where multiple sequences are aligned •This alignment provides insights not possible in pairwise alignments, such as •Conserved sequence patterns •Conserved and functionally critical amino acid residues •Prerequisite for phylogenetic analyses ...
PTC bioinformatics
... classmate was a taster, their DNA would be cleaved leaving a 44 and 177 base pair segment, which would be able to be seen through gel electrophoresis. What would be seen specifically in gel electrophoresis is a single stand for non tasters, and two split segments for those with the ability to taste ...
... classmate was a taster, their DNA would be cleaved leaving a 44 and 177 base pair segment, which would be able to be seen through gel electrophoresis. What would be seen specifically in gel electrophoresis is a single stand for non tasters, and two split segments for those with the ability to taste ...
What is Bioinformatics I?
... Phylogenetic analysis of molecular sequences with an emphasis on methods of phylogenetic inference and hypothesis testing. Gene and genome history, gene family evolution, inference of ancestral proteins, and phylogenetic analysis as a predictive tool. (3 weeks) ...
... Phylogenetic analysis of molecular sequences with an emphasis on methods of phylogenetic inference and hypothesis testing. Gene and genome history, gene family evolution, inference of ancestral proteins, and phylogenetic analysis as a predictive tool. (3 weeks) ...
Lecture3_HomologyAndAlignment2014_10sept
... is to be sequenced, the chromosomes from many cells are broken at random positions into small fragments, which are sequenced, and reassembled into long sequences (contigs). Contigs may be assembled into longer sequences called scaffolds and sometimes, if the depth of sequencing is high enough, there ...
... is to be sequenced, the chromosomes from many cells are broken at random positions into small fragments, which are sequenced, and reassembled into long sequences (contigs). Contigs may be assembled into longer sequences called scaffolds and sometimes, if the depth of sequencing is high enough, there ...
Genomes and sequence alignment
... Loci are referred to as "features", which can be anything Genes, introns/exons, polymorphisms, regulatory elements, conserved regions, islands, etc. Raw sequences don't have these (obviously!) Have to be added after the fact, usually first-pass computational, subsequently curated DBs differ by type ...
... Loci are referred to as "features", which can be anything Genes, introns/exons, polymorphisms, regulatory elements, conserved regions, islands, etc. Raw sequences don't have these (obviously!) Have to be added after the fact, usually first-pass computational, subsequently curated DBs differ by type ...
Bioinformatics Unit 1: Data Bases and Alignments
... Terminology Associated with Searches and Alignments (cont.) • Filters: usually part of an alignment algorithm and are turned on by default. – The filter masks (hides) regions of the query sequence (your sequence) that have low compositional complexity (like poly A tails). Masking is achieved by rep ...
... Terminology Associated with Searches and Alignments (cont.) • Filters: usually part of an alignment algorithm and are turned on by default. – The filter masks (hides) regions of the query sequence (your sequence) that have low compositional complexity (like poly A tails). Masking is achieved by rep ...
HIDDEN MARKOV MODELS
... • For example, identification of genes in the presence of exons/introns, gene features (CpG islands, etc.), domain profiles in ...
... • For example, identification of genes in the presence of exons/introns, gene features (CpG islands, etc.), domain profiles in ...
MultipleSequenceAlignment
... W in ClustalW refers to a weighting of scores depending on how far a sequence is from the root on the phylogenetic tree (See p. 154 of Bioinformatics by Mount.) ...
... W in ClustalW refers to a weighting of scores depending on how far a sequence is from the root on the phylogenetic tree (See p. 154 of Bioinformatics by Mount.) ...
Protein Evolution and Sequence Analysis
... Trp and Cys are uncommon, should those matches be given higher scores? ...
... Trp and Cys are uncommon, should those matches be given higher scores? ...
Sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.Sequence alignments are also used for non-biological sequences, such as those present in natural language or in financial data.