I. Comparing genome sequences
... • Involve substitutions with minimal or no functional impact • Fixed by random genetic drift ...
... • Involve substitutions with minimal or no functional impact • Fixed by random genetic drift ...
Biology and computers
... Understand how the Smith-Waterman algorithm can be applied to perform local alignment. Have a general understanding about PAM and BLOSUM ...
... Understand how the Smith-Waterman algorithm can be applied to perform local alignment. Have a general understanding about PAM and BLOSUM ...
Week4-Blast/MSA
... • A set of heuristics were applied to the above algorithm to make it less greedy, so it is less sensitive but runs faster • Implements Dynamic programming • Provide local alignment between two sequences • Both BLAST and FASTA use this algorithm with varying heuristics applied in each case ______ ...
... • A set of heuristics were applied to the above algorithm to make it less greedy, so it is less sensitive but runs faster • Implements Dynamic programming • Provide local alignment between two sequences • Both BLAST and FASTA use this algorithm with varying heuristics applied in each case ______ ...
lecture05_09
... Rows represent individual sequences Columns represent ‘same’ position Gaps allowed in all sequences ...
... Rows represent individual sequences Columns represent ‘same’ position Gaps allowed in all sequences ...
Protein Sequence Alignment and Database Searching
... –Expected Value (E), Chances that non-related sequence may have that score ...
... –Expected Value (E), Chances that non-related sequence may have that score ...
Pairwise sequence alignment - uni
... Pairwise alignment: protein sequences can be more informative than DNA • Protein is more informative (20 vs 4 characters); many amino acids share related biophysical properties • Codons are degenerate: changes in the third position often do not alter the amino acid that is specified • Protein se ...
... Pairwise alignment: protein sequences can be more informative than DNA • Protein is more informative (20 vs 4 characters); many amino acids share related biophysical properties • Codons are degenerate: changes in the third position often do not alter the amino acid that is specified • Protein se ...
Lecture 8
... increase the speed of the program used to make alignments. Heuristic algorithms are based on how proteins evolve. Risk= may get suboptimal results. PAM-250 Matrix is based on extrapolation: calculation assumes 1 PAM unit of evolutionary distance is the same as 250 PAM units. Because proteins can evo ...
... increase the speed of the program used to make alignments. Heuristic algorithms are based on how proteins evolve. Risk= may get suboptimal results. PAM-250 Matrix is based on extrapolation: calculation assumes 1 PAM unit of evolutionary distance is the same as 250 PAM units. Because proteins can evo ...
Learning objectives for Sequence Analysis 1
... compared to every sequence in a sequence database, and the similar ones are identified. Alignments with the best-matching sequences are shown and scored. If a query sequence can be readily aligned to a database sequence of known function, structure, or biochemical activity, the query sequence is pre ...
... compared to every sequence in a sequence database, and the similar ones are identified. Alignments with the best-matching sequences are shown and scored. If a query sequence can be readily aligned to a database sequence of known function, structure, or biochemical activity, the query sequence is pre ...
tutorialdm
... rearrangement occurring in many different diseases. This information can be of different type. 1) Using one of the species it is possible to transfer annotation information that were not known in the other species, 2) identify region that are under selective pressure, 3) It is also possible to ...
... rearrangement occurring in many different diseases. This information can be of different type. 1) Using one of the species it is possible to transfer annotation information that were not known in the other species, 2) identify region that are under selective pressure, 3) It is also possible to ...
LEQ: How does RNA help to make a protein?
... The type of RNA that carriers the genetic information/message from DNA and coveys it to ribosomes where the information is translated into amino acid sequences ...
... The type of RNA that carriers the genetic information/message from DNA and coveys it to ribosomes where the information is translated into amino acid sequences ...
I. Comparing genome sequences
... • Involve substitutions with minimal or no functional impact • Fixed by random genetic drift ...
... • Involve substitutions with minimal or no functional impact • Fixed by random genetic drift ...
Phylogenetic tree estimation
... The study of the relationship of genome structure and function across different biological species or strains. ...
... The study of the relationship of genome structure and function across different biological species or strains. ...
final exam in kje-2004
... conclusion is based on the similarity between a pair of sequences. There is never a degree of homology. Sequence similarity: a quantitative measure between two sequences in an alignment. The similarity can be presented as for example percentage similarity. Sequence identity: a quantitative measure b ...
... conclusion is based on the similarity between a pair of sequences. There is never a degree of homology. Sequence similarity: a quantitative measure between two sequences in an alignment. The similarity can be presented as for example percentage similarity. Sequence identity: a quantitative measure b ...
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 ...
Diapositiva 1 - Universitat de Lleida
... searches through this solution space. • The score for a given alignment of all the sequences is the sum of the scores for each pair, where each of the pair-wise scores is multiplied by a weight є indicating how far the pair-wise score differs from the first-cut msa alignment score. ...
... searches through this solution space. • The score for a given alignment of all the sequences is the sum of the scores for each pair, where each of the pair-wise scores is multiplied by a weight є indicating how far the pair-wise score differs from the first-cut msa alignment score. ...
Bioinformatics Unit 1: Data Bases and Alignments
... • Groups of genes or proteins from different organisms that have the same function are ...
... • Groups of genes or proteins from different organisms that have the same function are ...
Sequencing genomes
... • However, gaps can be inserted to get something like this insertion × deletion indel ...
... • However, gaps can be inserted to get something like this insertion × deletion indel ...
Classification of DNA sequences using Bloom Filters
... • A new algorithm(FACS) to classify sequences as belonging or not belonging to a reference sequence • Source code available at; – http://facs.biotech.kth.se ...
... • A new algorithm(FACS) to classify sequences as belonging or not belonging to a reference sequence • Source code available at; – http://facs.biotech.kth.se ...
- Covenant University Repository
... aligning with other sequences whose function and structure is already known. However, finding an optimal multiple sequence alignment takes time and space exponential with the length or number of sequences increases. Genetic Algorithms (GAs) are strategies of random searching that optimize an objecti ...
... aligning with other sequences whose function and structure is already known. However, finding an optimal multiple sequence alignment takes time and space exponential with the length or number of sequences increases. Genetic Algorithms (GAs) are strategies of random searching that optimize an objecti ...
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 ...
Document
... is a relatively straightforward computational problem. There are lots of possible alignments. Two sequences can always be aligned. ...
... is a relatively straightforward computational problem. There are lots of possible alignments. Two sequences can always be aligned. ...
Multiple sequence alignment
A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acids or nucleotides.Multiple sequence alignment also refers to the process of aligning such a sequence set. Because three or more sequences of biologically relevant length can be difficult and are almost always time-consuming to align by hand, computational algorithms are used to produce and analyze the alignments. MSAs require more sophisticated methodologies than pairwise alignment because they are more computationally complex. Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive.