Nucleotide sequence analysis - Bioinformatics Unit
... •Is it contaminated with vector sequences? •Is it an already known gene? •Is it related to any other genes either by having a common ancestor? •Is it similar in function to other genes via convergent evolution? •What could the protein sequence be for this nucleotide fra ...
... •Is it contaminated with vector sequences? •Is it an already known gene? •Is it related to any other genes either by having a common ancestor? •Is it similar in function to other genes via convergent evolution? •What could the protein sequence be for this nucleotide fra ...
Bio499 Bioinformatics
... analysis using only frame 1. Remove all other report outputs by selecting 0 or none or restriction enzymes of 8+. Print the report with the DNA and protein sequence aligned together (you may try to use other translation program as long as the report can lay out the translated protein sequence under ...
... analysis using only frame 1. Remove all other report outputs by selecting 0 or none or restriction enzymes of 8+. Print the report with the DNA and protein sequence aligned together (you may try to use other translation program as long as the report can lay out the translated protein sequence under ...
No Slide Title
... Provides details about ordered and oriented contigs, and accurate placement in the finished sequence. ...
... Provides details about ordered and oriented contigs, and accurate placement in the finished sequence. ...
Lecture 10 - University of New England
... • An alignment of sequences is intrinsically connected with another essential task, which is finding certain signals and motifs (highly conservative ungapped blocks) shared by some sequences. • A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences. Motif ...
... • An alignment of sequences is intrinsically connected with another essential task, which is finding certain signals and motifs (highly conservative ungapped blocks) shared by some sequences. • A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences. Motif ...
Catalogue of Expressed Sequence Tags (ESTs) from
... Glycyphagus domesticus had an additional 8 allergens distinct to itself. These were dust mite allergen groups 5 and7, tropomyosin and superoxide dismutase. It also contained allergens from other organisms such as plants (Juniperus virginiana and Hevea brasiliensis), yeast (Malassezia sympodialis), a ...
... Glycyphagus domesticus had an additional 8 allergens distinct to itself. These were dust mite allergen groups 5 and7, tropomyosin and superoxide dismutase. It also contained allergens from other organisms such as plants (Juniperus virginiana and Hevea brasiliensis), yeast (Malassezia sympodialis), a ...
such as for example in pairwise distance methods
... This is a critical step in the analysis as in many cases the alignment of amino acids or nucleotides in a column implies that they share a common ancestor ...
... This is a critical step in the analysis as in many cases the alignment of amino acids or nucleotides in a column implies that they share a common ancestor ...
Genome Evolution, Chromosomal Mutations, Paralogy
... Dynamic program based on the recurrence relationship: score(Bi) = max(score(Bj) + match(Bi) - gap(Bi, Bj)) ...
... Dynamic program based on the recurrence relationship: score(Bi) = max(score(Bj) + match(Bi) - gap(Bi, Bj)) ...
NOTE Phylogenetic analysis of Gram
... events that produced bifunctional proteins provide the most definitive markers of evolutionary branching among bacterial groupings that diverged at nearly the same time (Ahmad & Jensen, 1988, 1989 ; Jensen & Ahmad, 1990). However, gene-fusion events are rare and are thus of limited use in determinin ...
... events that produced bifunctional proteins provide the most definitive markers of evolutionary branching among bacterial groupings that diverged at nearly the same time (Ahmad & Jensen, 1988, 1989 ; Jensen & Ahmad, 1990). However, gene-fusion events are rare and are thus of limited use in determinin ...
BIO4342 Exercise 1: Detecting and Interpreting Genetic Homology
... the entire protein matched? If not, which residues are missing? Are any regions of the protein matched more than once at different places in the query sequence? You should see a considerable amount of confusion in this BLAST output – missing residues, duplicated residues, etc. As an annotator, your ...
... the entire protein matched? If not, which residues are missing? Are any regions of the protein matched more than once at different places in the query sequence? You should see a considerable amount of confusion in this BLAST output – missing residues, duplicated residues, etc. As an annotator, your ...
Slide 1
... Genetics of rare developmental phenotypes (analysis of de novo mutations that cannot be mapped by genetic techniques) Genetics of model organisms (identification of genes involved in diverse processes by mutagenesis screens) Genomics and evolutionary genetics (e.g., quantifying ...
... Genetics of rare developmental phenotypes (analysis of de novo mutations that cannot be mapped by genetic techniques) Genetics of model organisms (identification of genes involved in diverse processes by mutagenesis screens) Genomics and evolutionary genetics (e.g., quantifying ...
lecture9 - Stanford AI Lab
... detect miRNAs in animals based on both sequence and structure alignment ...
... detect miRNAs in animals based on both sequence and structure alignment ...
Document
... – The matrix values are based on 2000 conserved amino acid patterns (blocks) - pairwise comparisons —> more efficient for distantly related proteins —> more agreement with 3D structure data BLOSUM62 - 62% minimum sequence identity (BlastP default) BLOSUM50 - 50% minimum sequence identity BLOSUM42 - ...
... – The matrix values are based on 2000 conserved amino acid patterns (blocks) - pairwise comparisons —> more efficient for distantly related proteins —> more agreement with 3D structure data BLOSUM62 - 62% minimum sequence identity (BlastP default) BLOSUM50 - 50% minimum sequence identity BLOSUM42 - ...
Nucleotide substitutions and evolution of duplicate genes.
... This paper describes the software we developed for these experiments The next section is a description of a program that compares large numbers of pairs of genes. The input to the program is a stream of aligned amino acid sequences, and the output is a set of aligned nucleotide sequences with codons ...
... This paper describes the software we developed for these experiments The next section is a description of a program that compares large numbers of pairs of genes. The input to the program is a stream of aligned amino acid sequences, and the output is a set of aligned nucleotide sequences with codons ...
lab6
... • TwinScan finds genes in a "target" genomic sequence by simultaneously maximizing the probability of the gene structure in the target and the evolutionary conservation derived from "informant" genomic sequences. • The target sequence (i.e. the sequence to be annotated) should generally be of draft ...
... • TwinScan finds genes in a "target" genomic sequence by simultaneously maximizing the probability of the gene structure in the target and the evolutionary conservation derived from "informant" genomic sequences. • The target sequence (i.e. the sequence to be annotated) should generally be of draft ...
slides - Yin Lab @ NIU
... running (Windows) or a shell terminal is running (Ubuntu) … In any case, you have to close the terminal session (or have it be automatically terminated by the server). If this happens, your program will be terminated without finishing. If you expect your program will run for a very long time, e.g. l ...
... running (Windows) or a shell terminal is running (Ubuntu) … In any case, you have to close the terminal session (or have it be automatically terminated by the server). If this happens, your program will be terminated without finishing. If you expect your program will run for a very long time, e.g. l ...
Combining Machine Learning and Homology-Based
... • Terminal-Based N-Center-C (“Three-Part”) Composition. Many proteins in the cell contain important signal peptides at their N- or C-terminal region, which determine the subcellular location of the protein. It is not a simple task to directly identify these signal peptides from the sequence. Instead ...
... • Terminal-Based N-Center-C (“Three-Part”) Composition. Many proteins in the cell contain important signal peptides at their N- or C-terminal region, which determine the subcellular location of the protein. It is not a simple task to directly identify these signal peptides from the sequence. Instead ...
Text S1, DOCX file, 0.03 MB
... transposase and inactivated derivatives, while the second one coded for a putative efflux pump. However, we found significant support of paired reads extending both upstream and downstream of these regions into regions of scaffold with average coverage. Blastp analyses indicated that proteins in the ...
... transposase and inactivated derivatives, while the second one coded for a putative efflux pump. However, we found significant support of paired reads extending both upstream and downstream of these regions into regions of scaffold with average coverage. Blastp analyses indicated that proteins in the ...
DNA ANALYSIS: Public vs private access to the human genome
... (underlined and in blue) to open the database file. Assignment Part 1. a. Print out a copy of your assigned zebrafish cDNA sequence. To obtain a hard copy of your data, your computer must be connected to a printer. Click on the print button located in the top center of your web browser. If you do no ...
... (underlined and in blue) to open the database file. Assignment Part 1. a. Print out a copy of your assigned zebrafish cDNA sequence. To obtain a hard copy of your data, your computer must be connected to a printer. Click on the print button located in the top center of your web browser. If you do no ...
ADOPS - Automatic Detection Of Positively Selected Sites 1
... the transeq tool available in the EMBOSS package) and aligned at the amino acid level using T-Coffee [39, 41], a resourceful multiple sequence alignment (MSA) software. T-Coffee allows the user to align sequences using third party aligners and provides a metamethod to combine the output of several i ...
... the transeq tool available in the EMBOSS package) and aligned at the amino acid level using T-Coffee [39, 41], a resourceful multiple sequence alignment (MSA) software. T-Coffee allows the user to align sequences using third party aligners and provides a metamethod to combine the output of several i ...
Document
... – The matrix values are based on 2000 conserved amino acid patterns (blocks) - pairwise comparisons —> more efficient for distantly related proteins —> more agreement with 3D structure data BLOSUM62 - 62% minimum sequence identity (BlastP default) BLOSUM50 - 50% minimum sequence identity BLOSUM42 - ...
... – The matrix values are based on 2000 conserved amino acid patterns (blocks) - pairwise comparisons —> more efficient for distantly related proteins —> more agreement with 3D structure data BLOSUM62 - 62% minimum sequence identity (BlastP default) BLOSUM50 - 50% minimum sequence identity BLOSUM42 - ...
alignable - gobics.de: Department of Bioinformatics
... Gene-regulatory sites identified by mulitple sequence alignment (phylogenetic footprinting) ...
... Gene-regulatory sites identified by mulitple sequence alignment (phylogenetic footprinting) ...
Kernels for gene regulatory regions
... the concatenation of the available promoter regions—ignoring, however, k-mers that overlap different sequences in the concatenation. The rationale behind this kernel, compared to the spectrum kernel, is two-fold. First, if all promoters contain common functional motifs and randomly varying nonfuncti ...
... the concatenation of the available promoter regions—ignoring, however, k-mers that overlap different sequences in the concatenation. The rationale behind this kernel, compared to the spectrum kernel, is two-fold. First, if all promoters contain common functional motifs and randomly varying nonfuncti ...
Lecture4 - Department of Computer Science
... Which Similarity Matrix to Use? • Database searches or sequence alignments perform much better if the similarity matrix is based on replacement patterns that correspond to the degree of divergence of the sequences being aligned or discovered. • In database searching, a PAM or Blosum matrix correspon ...
... Which Similarity Matrix to Use? • Database searches or sequence alignments perform much better if the similarity matrix is based on replacement patterns that correspond to the degree of divergence of the sequences being aligned or discovered. • In database searching, a PAM or Blosum matrix correspon ...
Sequence Note vpu and env Sequence V ariability of HIV
... chosen for virus isolation by cocultivation with HIV -negative donor PBLs. Viral DNA sequences between the positions 5543 and 6956 (according to the HIV -1 Lai 2 sequence) were amplified by polymerase chain reaction (PCR), using two sets of primer pairs, subcloned into a Bluescript vector, and seque ...
... chosen for virus isolation by cocultivation with HIV -negative donor PBLs. Viral DNA sequences between the positions 5543 and 6956 (according to the HIV -1 Lai 2 sequence) were amplified by polymerase chain reaction (PCR), using two sets of primer pairs, subcloned into a Bluescript vector, and seque ...
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.