Sequence Analysis
... Here we consider the access and analysis of data and information items rather than their generation, storage or annotation ...
... Here we consider the access and analysis of data and information items rather than their generation, storage or annotation ...
Finding Patterns in Protein Sequence and Structure
... sequence, how can we determine the counts? – key insight: estimate the counts by considering every path weighted by its probability ...
... sequence, how can we determine the counts? – key insight: estimate the counts by considering every path weighted by its probability ...
FAST Lab Group Meeting 4/11/06
... Non-negative Matrix Factorization • NMF maintains the interpretability of components of data like images or text or spectra (SDSS) • However as a low-D display it is not faithful in general to the original distances • Isometric NMF [Vasiloglou, Gray, Anderson, to be submitted SIAM DM 2008] preserves ...
... Non-negative Matrix Factorization • NMF maintains the interpretability of components of data like images or text or spectra (SDSS) • However as a low-D display it is not faithful in general to the original distances • Isometric NMF [Vasiloglou, Gray, Anderson, to be submitted SIAM DM 2008] preserves ...
yanting-talk
... capture the constant row model • The scores for the range support patterns in RAP3 and RAP5 are almost all zero, with very few outliers. On the other hand, CC1 patterns have a much wider variability of these scores. ...
... capture the constant row model • The scores for the range support patterns in RAP3 and RAP5 are almost all zero, with very few outliers. On the other hand, CC1 patterns have a much wider variability of these scores. ...
Quiz 4 1 Recurrence Relation Approach
... Induction Step: Suppose an < an+1 . Then, this implies 2an < 2an+1 , since multiplication by 2 and square roots preserve inequality (the functions are increasing on x > 0). Substituting equivalent terms from the recurrence relation, we find an+1 < an+2 . By induction, the sequence is monotone increa ...
... Induction Step: Suppose an < an+1 . Then, this implies 2an < 2an+1 , since multiplication by 2 and square roots preserve inequality (the functions are increasing on x > 0). Substituting equivalent terms from the recurrence relation, we find an+1 < an+2 . By induction, the sequence is monotone increa ...
Aircraft Landing Problem
... Although the formulations given above for both the single- and multiplerunway cases are sufficient to describe the problems, we intend solving them numerically through the use of LP-based tree search. Relaxing the zero-one variables ...
... Although the formulations given above for both the single- and multiplerunway cases are sufficient to describe the problems, we intend solving them numerically through the use of LP-based tree search. Relaxing the zero-one variables ...
Instructions fro BLAST Alignment of sequences
... DNA strand is broken, the BRCA1 protein works with other proteins to help repair the break. If these breaks are not repaired, the DNA damage can ultimately lead to cancer. Therefore, BRCA1 is known as a tumor suppressor, because it helps prevent the formation of tumors (which can arise when DNA erro ...
... DNA strand is broken, the BRCA1 protein works with other proteins to help repair the break. If these breaks are not repaired, the DNA damage can ultimately lead to cancer. Therefore, BRCA1 is known as a tumor suppressor, because it helps prevent the formation of tumors (which can arise when DNA erro ...
File formats for NGS data - Bioinformatics Training Materials
... SAM header contains information on alignment and contigs used @HD - Version number and sorting information @SQ - Contig/Chromosome name and length of sequence ...
... SAM header contains information on alignment and contigs used @HD - Version number and sorting information @SQ - Contig/Chromosome name and length of sequence ...
Similarity Searches on Sequence Databases: BLAST
... • However this assumption doesn’t hold all the time, some sequences have biased compositions, e.g. many proteins contain patches known as low-complexity regions: such as segments that contain many prolines or glutamic acid residues. • If BLAST aligns two proline-rich domains, this alignment gets a v ...
... • However this assumption doesn’t hold all the time, some sequences have biased compositions, e.g. many proteins contain patches known as low-complexity regions: such as segments that contain many prolines or glutamic acid residues. • If BLAST aligns two proline-rich domains, this alignment gets a v ...
statgen9
... to express variation at a position in a gene during evolution to express ability of an enzyme to tolerate more than one base at a given position of a recognition site ...
... to express variation at a position in a gene during evolution to express ability of an enzyme to tolerate more than one base at a given position of a recognition site ...
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 ...
Bioinformatics - University of Colorado Denver
... meaning that it contains what NCBI determines is the strongest sequence data for each gene. Finally, we will be learning to use ClustalW, which is a multiple sequence alignment program. It allows you to enter a series of gene or protein sequences that you believe are similar and may be evolutionaril ...
... meaning that it contains what NCBI determines is the strongest sequence data for each gene. Finally, we will be learning to use ClustalW, which is a multiple sequence alignment program. It allows you to enter a series of gene or protein sequences that you believe are similar and may be evolutionaril ...
PPT1
... • Align all sequences (using multiple sequence alignment). • Compute the frequency of each nucleotide in each position (PSPM). • Incorporate background frequency for each nucleotide (PSSM). ...
... • Align all sequences (using multiple sequence alignment). • Compute the frequency of each nucleotide in each position (PSPM). • Incorporate background frequency for each nucleotide (PSSM). ...
Comparison of DNA Sequences with Protein Sequences
... they can be more easily joined, and (b) to allow small overlaps (10 residues) between joined regions. Step 4 is changed to produce a band-limited DNA–protein local alignment score (Zhang et al., 1997) as outlined above. FASTX and FASTY use a full Smith–Waterman local DNA–protein alignment in linear ...
... they can be more easily joined, and (b) to allow small overlaps (10 residues) between joined regions. Step 4 is changed to produce a band-limited DNA–protein local alignment score (Zhang et al., 1997) as outlined above. FASTX and FASTY use a full Smith–Waterman local DNA–protein alignment in linear ...
