Woods Hole – Zebrafish Genetics and Development Bioinformatics
... from analyzing conserved syntenies, in which gene content on particular chromosomes has been retained after species divergence. A useful viewer of conserved syntenies in multiple organisms can be found at the Oxgrid website: http://oxgrid.angis.org.au/oxg_table.html ...
... from analyzing conserved syntenies, in which gene content on particular chromosomes has been retained after species divergence. A useful viewer of conserved syntenies in multiple organisms can be found at the Oxgrid website: http://oxgrid.angis.org.au/oxg_table.html ...
Why do more divergent sequences produce smaller non
... lower than the corresponding synonymous distance (dS , measured by the number of synonymous substitutions per synonymous site), because the structure and function of a protein imposes constraints on the types of nonsynonymous (amino acid) substitutions that can take place, while synonymous substitut ...
... lower than the corresponding synonymous distance (dS , measured by the number of synonymous substitutions per synonymous site), because the structure and function of a protein imposes constraints on the types of nonsynonymous (amino acid) substitutions that can take place, while synonymous substitut ...
annotation_tutorial
... The third part of the screen shows the currently annotated features and is currently empty. To start annotating our gene we have a look at the second part of the BLAST report. The text Expect(8) = e-126 tells us that BLAST found 8 correctly distributed hits in the genome sequence. Taken together the ...
... The third part of the screen shows the currently annotated features and is currently empty. To start annotating our gene we have a look at the second part of the BLAST report. The text Expect(8) = e-126 tells us that BLAST found 8 correctly distributed hits in the genome sequence. Taken together the ...
Bio 125 Lab Week 9: Relating Changes in Form to Changes in Genes
... search should return eight results; if you have fewer, check the numbers in the search against the numbers listed above and make sure they were all entered correctly. Import the sequences into your database. Use the first two columns of the Table 4 on page 11 and the list on the Nucleic Tools page t ...
... search should return eight results; if you have fewer, check the numbers in the search against the numbers listed above and make sure they were all entered correctly. Import the sequences into your database. Use the first two columns of the Table 4 on page 11 and the list on the Nucleic Tools page t ...
Annotation Practice Activity [Based on materials from the GEP
... The typical structure of a eurkaryotic gene consists of a promoter region and an open reading frame (ORF). Features of an ORF are: (1)the presence of a start codon, AUG; (2) a sequence of codons that results in a series of amino acid sequences in a putative polypeptide, and (3) a termination codon ( ...
... The typical structure of a eurkaryotic gene consists of a promoter region and an open reading frame (ORF). Features of an ORF are: (1)the presence of a start codon, AUG; (2) a sequence of codons that results in a series of amino acid sequences in a putative polypeptide, and (3) a termination codon ( ...
Brand, Veronica - Degenerate Primer Design using Computational Tools
... degenerate primers targeting 16S rRNA, as one might do for studying microbial diversity. This may not be a major limitation since 16S rRNA genes are generally more highly conserved than proteins; sequences may be sufficiently related to design primers manually. More significant limitations include t ...
... degenerate primers targeting 16S rRNA, as one might do for studying microbial diversity. This may not be a major limitation since 16S rRNA genes are generally more highly conserved than proteins; sequences may be sufficiently related to design primers manually. More significant limitations include t ...
Compressed q-gram Indexing for Highly Repetitive Biological
... A classical q-gram index is formed by a vocabulary comprising all the different substrings of length q in T , and for each of those q-grams, a posting list recording the positions in T where they appear, in increasing order. To reduce space, block addressing is used, that is, the text is divided int ...
... A classical q-gram index is formed by a vocabulary comprising all the different substrings of length q in T , and for each of those q-grams, a posting list recording the positions in T where they appear, in increasing order. To reduce space, block addressing is used, that is, the text is divided int ...
Surveying Saccharomyces Genomes to Identify Functional Elements
... petite-negative species Saccharomyces kluyveri (Table 1). Over 4.3 Mb of unassembled sequence was obtained, a sample sufficient for genomic exploration of the Saccharomyces genus. Comparisons of the nucleotide sequences (using BLASTN, Table 1) and inferred protein sequences (using BLASTX, Table 2) t ...
... petite-negative species Saccharomyces kluyveri (Table 1). Over 4.3 Mb of unassembled sequence was obtained, a sample sufficient for genomic exploration of the Saccharomyces genus. Comparisons of the nucleotide sequences (using BLASTN, Table 1) and inferred protein sequences (using BLASTX, Table 2) t ...
Spider Silk - Consortium for Mathematics and its Applications
... Spiders are classified in the animal kingdom as shown below: • Phylum Arthropoda (which includes insects, arachnids, and crustaceans) • Class Arachnida (which includes scorpions, mites and ticks) • Order Araneae (which contains thousands of spider species) Spiders are found worldwide and most are pr ...
... Spiders are classified in the animal kingdom as shown below: • Phylum Arthropoda (which includes insects, arachnids, and crustaceans) • Class Arachnida (which includes scorpions, mites and ticks) • Order Araneae (which contains thousands of spider species) Spiders are found worldwide and most are pr ...
Introduction to Bioinformatics
... Now, on to ORF Finder. Enter the accession number as described. What do you get? Why six gray boxes with blue blobs in them? Why not one gray box? Why not three? What reading frame is the biggest? Click on it. SQ3. Compare its amino acid sequence to that in the GenBank entry. Same? Different? Compa ...
... Now, on to ORF Finder. Enter the accession number as described. What do you get? Why six gray boxes with blue blobs in them? Why not one gray box? Why not three? What reading frame is the biggest? Click on it. SQ3. Compare its amino acid sequence to that in the GenBank entry. Same? Different? Compa ...
repetitive extragenic palindromic sequences in pseudomonas
... following negatively oriented REP sequences shared another sequence Considering the conserved palindromy of REP sequences and the conserved arrangement of the clusters it is probable that REP sequences adopt conformations with peculiar secondary structures especially suitable to be specifically reco ...
... following negatively oriented REP sequences shared another sequence Considering the conserved palindromy of REP sequences and the conserved arrangement of the clusters it is probable that REP sequences adopt conformations with peculiar secondary structures especially suitable to be specifically reco ...
A set reduction and pattern matching problem motivated by Allele
... the pool of family specific sequences contains representatives from different loci, and each locus is expected to contain regions specific to itself. To design a primer in these locus specific regions they must first be identified. This requires a technique to 1) to cluster the sequences correspondi ...
... the pool of family specific sequences contains representatives from different loci, and each locus is expected to contain regions specific to itself. To design a primer in these locus specific regions they must first be identified. This requires a technique to 1) to cluster the sequences correspondi ...
Bioinformatics Database Worksheet
... search, in the colors that signify their BLAST scores, are located for you on the diagram. Notice that there are about 100 proteins (discovered so far, that is) that have 40% or more positives in alignment with red opsin. The opsins are members of the very large family of G protein-coupled receptors ...
... search, in the colors that signify their BLAST scores, are located for you on the diagram. Notice that there are about 100 proteins (discovered so far, that is) that have 40% or more positives in alignment with red opsin. The opsins are members of the very large family of G protein-coupled receptors ...
Genome
... In this exercise, we will use BLAST (Basic Local Alignment Search Tool) to search for significant occurrences of a class of transposable elements (TEs) called Short INterspersed Elements (SINEs), specifically of the ALU family, in the well-known VHL tumor suppressor gene. The goal of this exercise i ...
... In this exercise, we will use BLAST (Basic Local Alignment Search Tool) to search for significant occurrences of a class of transposable elements (TEs) called Short INterspersed Elements (SINEs), specifically of the ALU family, in the well-known VHL tumor suppressor gene. The goal of this exercise i ...
introduction to molecular phylogeny
... the alignment (site) is supposed to contain homologous residues (nucleotides, amino acids) that derive from a common ancestor. ==> Unreliable parts of the alignment must be omitted from further phylogenetic analysis. ...
... the alignment (site) is supposed to contain homologous residues (nucleotides, amino acids) that derive from a common ancestor. ==> Unreliable parts of the alignment must be omitted from further phylogenetic analysis. ...
DNA Sequence Capture and Enrichment by Microarray Followed by
... sequencing applications, such as targeted resequencing, whole-genome de novo sequencing, transcriptome sequencing, and microRNA profiling (1–5 ). Targeted resequencing of an extremely large gene or multiple disease-related genes has the unique advantage of allowing the identification of genetic alte ...
... sequencing applications, such as targeted resequencing, whole-genome de novo sequencing, transcriptome sequencing, and microRNA profiling (1–5 ). Targeted resequencing of an extremely large gene or multiple disease-related genes has the unique advantage of allowing the identification of genetic alte ...
Document
... In this exercise, we will use BLAST (Basic Local Alignment Search Tool) to search for significant occurrences of a class of transposable elements (TEs) called Short INterspersed Elements (SINEs), specifically of the ALU family, in the well-known VHL tumor suppressor gene. The goal of this exercise i ...
... In this exercise, we will use BLAST (Basic Local Alignment Search Tool) to search for significant occurrences of a class of transposable elements (TEs) called Short INterspersed Elements (SINEs), specifically of the ALU family, in the well-known VHL tumor suppressor gene. The goal of this exercise i ...
Milestone2
... The GC content of a genome is the percentage of nucleotides in the genome that are either guanines or cytosines. Different genomes have widely varying GC contents. For example, the genomes of the bacteria Anaeromyxobacter have a GC content of about 75%, whereas the genomes of the bacteria Buchnera h ...
... The GC content of a genome is the percentage of nucleotides in the genome that are either guanines or cytosines. Different genomes have widely varying GC contents. For example, the genomes of the bacteria Anaeromyxobacter have a GC content of about 75%, whereas the genomes of the bacteria Buchnera h ...
A simple set of rules for primer sequence design is as follows
... The optimum length of a primer depends upon its (A+T) content, and the Tm. Apart from the Tm, a prime consideration is that the primers should be complex enough so that the likelihood of annealing to sequences other than the chosen target is very low. For example, there is a ¼ chance of finding an A ...
... The optimum length of a primer depends upon its (A+T) content, and the Tm. Apart from the Tm, a prime consideration is that the primers should be complex enough so that the likelihood of annealing to sequences other than the chosen target is very low. For example, there is a ¼ chance of finding an A ...
Mapping strategies for sequence reads (with focus on RNA-seq)
... potential donor/acceptor splice sites within neighboring regions are joined ...
... potential donor/acceptor splice sites within neighboring regions are joined ...
Presentation
... • Clustal-W performs multialignment • Aligns – The originating IMAS gene sequence – The “Full” sequence found by BLAST • Not just the high-quality section – Useful to align entire genes, or entire corresponding segments of DNA ...
... • Clustal-W performs multialignment • Aligns – The originating IMAS gene sequence – The “Full” sequence found by BLAST • Not just the high-quality section – Useful to align entire genes, or entire corresponding segments of DNA ...
Identification of logical extra-ribosomal functions
... Clustal X is a multiple sequence alignment programs that have been completely rewritten in C++ with a simple object model in order to make it easier to maintain the code and more importantly to make it easier to modify or even replace some of the alignment algorithm (Larkin et al., 2007). Clustal X ...
... Clustal X is a multiple sequence alignment programs that have been completely rewritten in C++ with a simple object model in order to make it easier to maintain the code and more importantly to make it easier to modify or even replace some of the alignment algorithm (Larkin et al., 2007). Clustal X ...
Slide 1
... Which bacterial species have a protein that is related in lineage to another protein? What other genes encode proteins that exhibit structures or motifs such as ones that have just been determined? ...
... Which bacterial species have a protein that is related in lineage to another protein? What other genes encode proteins that exhibit structures or motifs such as ones that have just been determined? ...
Uniprot - European Bioinformatics Institute
... • Ensembl and UniProt collaboration to cover the gaps in gene predictions in UniProtKB (one sequence for each protein coding transcript in Ensembl) • Ensembl high quality gene/transcript models (quality checks remove gene models with erroneous structures or supported by dubious evidence – e.g. cDNA ...
... • Ensembl and UniProt collaboration to cover the gaps in gene predictions in UniProtKB (one sequence for each protein coding transcript in Ensembl) • Ensembl high quality gene/transcript models (quality checks remove gene models with erroneous structures or supported by dubious evidence – e.g. cDNA ...
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.