Comparative Sequence Analysis between Human and Mouse
... DBTSS provides a representative TSS for each gene in human and mouse genomes, and an orthologous table for comparison of TSS data. In this study, sequences from -1000 to +200 based on the representative TSSs were defined as promoter sequences. Protein sequences were obtained from NCBI reference sequ ...
... DBTSS provides a representative TSS for each gene in human and mouse genomes, and an orthologous table for comparison of TSS data. In this study, sequences from -1000 to +200 based on the representative TSSs were defined as promoter sequences. Protein sequences were obtained from NCBI reference sequ ...
Faik Bioinformatics PowerPoint 2-2006
... contrast, maximum likelihood does not necessarily satisfy any optimality criterion. It attempts to answer the question: What parameters of evolutionary events was likely to produce the current data set? This is computationally difficult to do. This is the slowest of all methods. ...
... contrast, maximum likelihood does not necessarily satisfy any optimality criterion. It attempts to answer the question: What parameters of evolutionary events was likely to produce the current data set? This is computationally difficult to do. This is the slowest of all methods. ...
Slides 4 - UF CISE - University of Florida
... • Different levels of the BLOSUM matrix can be created by differentially weighting the degree of similarity between sequences. For example, a BLOSUM62 matrix is calculated from protein blocks such that if two sequences are more than 62% identical, then the contribution of these sequences is weighted ...
... • Different levels of the BLOSUM matrix can be created by differentially weighting the degree of similarity between sequences. For example, a BLOSUM62 matrix is calculated from protein blocks such that if two sequences are more than 62% identical, then the contribution of these sequences is weighted ...
Solving Multiple Sequence Alignment Problems using Various E
... When DNA or RNA sequences are placed together, it is seen that there reflects an interesting effect of alignment which is known as sequence alignment. Many bioinformatics tasks depend upon successful alignments. In a symbolic sequence, a letter signifies each base or residue monomer in each sequence ...
... When DNA or RNA sequences are placed together, it is seen that there reflects an interesting effect of alignment which is known as sequence alignment. Many bioinformatics tasks depend upon successful alignments. In a symbolic sequence, a letter signifies each base or residue monomer in each sequence ...
Introduction to BLAST
... R. Bjornson et al. (2002). TurboBLAST®: A parallel implementation of BLAST built on the TurboHub, Proc. International Parallel and Distributed Processing Symposium. A. Darling, L. Carey and W.C. Feng (2003). The design, implementation, and evaluation of mpiBLAST, Proc. ...
... R. Bjornson et al. (2002). TurboBLAST®: A parallel implementation of BLAST built on the TurboHub, Proc. International Parallel and Distributed Processing Symposium. A. Darling, L. Carey and W.C. Feng (2003). The design, implementation, and evaluation of mpiBLAST, Proc. ...
Name
... 3. When you have completed your comparisons, enter the number of differences in the data table below. List the eight vertebrates in order from fewest differences to the most differences from humans. ...
... 3. When you have completed your comparisons, enter the number of differences in the data table below. List the eight vertebrates in order from fewest differences to the most differences from humans. ...
Text S1. Predicted Functional RNAs Within Coding Regions
... is no underlying statistical model. Although RNAz utilizes an SCI-value to measure structural conservation between aligned sequences and a z-score to measure thermodynamic stability, the p-value provides the user a more comprehensive value for final classification. More specifically, RNAz uses an ad ...
... is no underlying statistical model. Although RNAz utilizes an SCI-value to measure structural conservation between aligned sequences and a z-score to measure thermodynamic stability, the p-value provides the user a more comprehensive value for final classification. More specifically, RNAz uses an ad ...
wg: Use primers wg550F and wgABRZ with cycler profile ST
... yield sequences for the majority of the family. Unless otherwise noted, sequencing primers are the same as amplification primers. Refer to table S6 Table for cycling protocol and S2 Table for details about primers. 18S: Use primer pair 518S and S1893R with cycler profile ST-50-C. Aliquot PCR product ...
... yield sequences for the majority of the family. Unless otherwise noted, sequencing primers are the same as amplification primers. Refer to table S6 Table for cycling protocol and S2 Table for details about primers. 18S: Use primer pair 518S and S1893R with cycler profile ST-50-C. Aliquot PCR product ...
Linear time algorithm for parsing RNA secondary structure
... → Local alignment search tool → performing sequence-similarity searches against variety of sequence databases → returning a set of gapped alignments btw the query and database sequences ...
... → Local alignment search tool → performing sequence-similarity searches against variety of sequence databases → returning a set of gapped alignments btw the query and database sequences ...
生物信息学主要英文术语及释义
... Refers to the procedure of comparing two or more sequences by looking for a series of individual characters or character patterns that are in the same order in the sequences. Of the two types of alignment, local and global, a local alignment is generally the most useful. See also Local and Global al ...
... Refers to the procedure of comparing two or more sequences by looking for a series of individual characters or character patterns that are in the same order in the sequences. Of the two types of alignment, local and global, a local alignment is generally the most useful. See also Local and Global al ...
DBMS-based EST Clustering and Profiling for Gene Expression
... discovery of candidate genes with similar functions, and tissues and cells with mit similar expression profiles ...
... discovery of candidate genes with similar functions, and tissues and cells with mit similar expression profiles ...
Introduction to Biological Data
... 1a Locus Name (HSHFE) - The locus name is a tag for grouping similar sequences. The first two or three letters usually designate the organism. In this case HS stands for Homo sapiens The last several characters are associated with another group designation, such as gene product. In this example, the ...
... 1a Locus Name (HSHFE) - The locus name is a tag for grouping similar sequences. The first two or three letters usually designate the organism. In this case HS stands for Homo sapiens The last several characters are associated with another group designation, such as gene product. In this example, the ...
BI-Lec 3
... Principal requirements of a database The principal requirements on the public data services are: • Data quality - data quality has to be of the highest priority. However, because the data services in most cases lack access to supporting data, the quality of the data must remain the primary responsib ...
... Principal requirements of a database The principal requirements on the public data services are: • Data quality - data quality has to be of the highest priority. However, because the data services in most cases lack access to supporting data, the quality of the data must remain the primary responsib ...
Molecular Phylogeny
... ..T.. more closely related to each other than they are to the sequence with G. ...
... ..T.. more closely related to each other than they are to the sequence with G. ...
ppt
... phylogenetic footprinting: • “fast”, higher levels of divergence as in neutral sequences • “slow”, divergence as in purifying selection) accounts for phylogenetic footprinting ...
... phylogenetic footprinting: • “fast”, higher levels of divergence as in neutral sequences • “slow”, divergence as in purifying selection) accounts for phylogenetic footprinting ...
PDF format Glossary of Search Items
... • 3’UTR variation • 5’UTR variation • intronic variation Mutation / polymorphism: Asks whether the sequence variation described is likely to be a mutation (capable of causing a diseased phenotype), a polymorphism (not capable of causing a diseased phenotype) or a silent polymorphism (a variation in ...
... • 3’UTR variation • 5’UTR variation • intronic variation Mutation / polymorphism: Asks whether the sequence variation described is likely to be a mutation (capable of causing a diseased phenotype), a polymorphism (not capable of causing a diseased phenotype) or a silent polymorphism (a variation in ...
Making a Phylogenetic Tree
... It would not be possible to analyze the mutations if the words with the same meanings had not first been aligned with each other. ...
... It would not be possible to analyze the mutations if the words with the same meanings had not first been aligned with each other. ...
Convergent_Evolution_instructor_edited
... each entry has an Accession number, a unique identifier that specifies the databank and number of the entry in that databank. 4. For each species, once you locate a search result in which the Accession number enter that number in Table 1. Then click on the FASTA link below the Accession number. This ...
... each entry has an Accession number, a unique identifier that specifies the databank and number of the entry in that databank. 4. For each species, once you locate a search result in which the Accession number enter that number in Table 1. Then click on the FASTA link below the Accession number. This ...
Illumin8er: Software for the Illumina GAII
... and 2 of 10 individuals. Each nucleotide had a read depth of at least 75 reads (approximately 6.6x103 sequences per gene). The alignment and mutation annotation took ~50 ...
... and 2 of 10 individuals. Each nucleotide had a read depth of at least 75 reads (approximately 6.6x103 sequences per gene). The alignment and mutation annotation took ~50 ...
Lec-GenomeAllignment2010
... Genome Alignment • Depending on level of similarity, genome alignments may need to contend with rearrangements and large-scale duplications and deletions • Draft or partial genomes can both benefit from and confound alignment • Need to visualize results in summary form ...
... Genome Alignment • Depending on level of similarity, genome alignments may need to contend with rearrangements and large-scale duplications and deletions • Draft or partial genomes can both benefit from and confound alignment • Need to visualize results in summary form ...
How does eukaryotic gene prediction work?
... followed by “s,” rare examples notwithstanding (Fig. 1a). An alternative hypothesis that solves this problem is that the sender intended to type “hot.” However, typing “o” for “s” is an unlikely error, as “o” is nowhere near “s” on the keyboard. A more likely hypothesis is that the sender intended t ...
... followed by “s,” rare examples notwithstanding (Fig. 1a). An alternative hypothesis that solves this problem is that the sender intended to type “hot.” However, typing “o” for “s” is an unlikely error, as “o” is nowhere near “s” on the keyboard. A more likely hypothesis is that the sender intended t ...
class10
... This class has been edited from Nir Friedman’s lecture. Changes made by Dan Geiger, then Shlomo Moran. ...
... This class has been edited from Nir Friedman’s lecture. Changes made by Dan Geiger, then Shlomo Moran. ...
Bioinformatics
... • Blastn: searches a nucleotide database using a nucleotide query. • Blastp: searches a protein database using a protein query. • Blastx: searches a protein database using a translated nucleotide query. • Tblastx: searches a translated nucleotide database using a translated nucleotide query. ...
... • Blastn: searches a nucleotide database using a nucleotide query. • Blastp: searches a protein database using a protein query. • Blastx: searches a protein database using a translated nucleotide query. • Tblastx: searches a translated nucleotide database using a translated nucleotide query. ...
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.