Mapping strategies for sequence reads (with focus on RNA-seq)
... PALMA pipeline has organizational similarities to are major differences. First, QPALMA uses a training uires a set of known junctions from the reference ond, the QPALMA pipeline’s initial mapping phase (Abouelhoda et al., 2004), a general-purpose suffix lignment program. Vmatch is a flexible, fast a ...
... PALMA pipeline has organizational similarities to are major differences. First, QPALMA uses a training uires a set of known junctions from the reference ond, the QPALMA pipeline’s initial mapping phase (Abouelhoda et al., 2004), a general-purpose suffix lignment program. Vmatch is a flexible, fast a ...
Distinguishing coding from non-coding sequences in a prokaryote
... a data set of 51 available bacterial genomes. Then, we use the global descriptor method on the coding/non-coding primary sequences and obtain 36 parameters for each coding/non-coding primary sequence. These parameters are used to generate some spaces, whose points represent coding/non-coding sequenc ...
... a data set of 51 available bacterial genomes. Then, we use the global descriptor method on the coding/non-coding primary sequences and obtain 36 parameters for each coding/non-coding primary sequence. These parameters are used to generate some spaces, whose points represent coding/non-coding sequenc ...
NOTE Phylogenetic analysis of Gram
... levels of amino acid identity near the N- and Cterminal ends of these grpE sequences (data not shown). The amino acid sequence alignment of the grpE homologues shown in Fig. 2 was used to examine the phylogenetic relationships between various Grampositive bacteria. A neighbour-joining consensus tree ...
... levels of amino acid identity near the N- and Cterminal ends of these grpE sequences (data not shown). The amino acid sequence alignment of the grpE homologues shown in Fig. 2 was used to examine the phylogenetic relationships between various Grampositive bacteria. A neighbour-joining consensus tree ...
PSI - Bioinformatics Training Network (BTN)
... UCSC and UniProt, aims to provide a standard set of gene predictions for the human and mouse genomes • Considerable communication effort between curators from different groups is on-going ...
... UCSC and UniProt, aims to provide a standard set of gene predictions for the human and mouse genomes • Considerable communication effort between curators from different groups is on-going ...
HiddenMarkovModels
... which the probabilities to have different amino acids are different (for example, it is very unlikely for members of the family to have an amino acid with hydrophilic residue in the hydrophobic region, or gly and pro are very likely to be present at sharp bends of the polypeptide chain, etc.). Diffe ...
... which the probabilities to have different amino acids are different (for example, it is very unlikely for members of the family to have an amino acid with hydrophilic residue in the hydrophobic region, or gly and pro are very likely to be present at sharp bends of the polypeptide chain, etc.). Diffe ...
Decomposition of DNA Sequence Complexity
... and thus, for a given sequence, a series of measures can be obtained depending on symbol grouping (mapping rule). This problem is especially acute for DNA, where a wide variety of mapping rules are usually employed [4]. We show here, however, that such measures are related by simple relationships, t ...
... and thus, for a given sequence, a series of measures can be obtained depending on symbol grouping (mapping rule). This problem is especially acute for DNA, where a wide variety of mapping rules are usually employed [4]. We show here, however, that such measures are related by simple relationships, t ...
MacVector 14.0 Getting Started Guide
... To set up automatic restriction enzyme site searching select MacVector | Preferences from the main menu, then click the Map View icon on the preferences dialog. Ensure that the Automatic RE Analysis box is checked. Click Set Enzyme File button to choose a restriction enzyme file for the automatic an ...
... To set up automatic restriction enzyme site searching select MacVector | Preferences from the main menu, then click the Map View icon on the preferences dialog. Ensure that the Automatic RE Analysis box is checked. Click Set Enzyme File button to choose a restriction enzyme file for the automatic an ...
Using dynamics-based comparisons to predict nucleic acid binding
... This preference corresponds to the same specificity observed for the full-length protein (Yue et al., 2001). HBP1_AXH (de Chiara et al., 2003; Yue et al., 2001) binds poly(rU) and poly(rA). Weaker or no binding was observed for poly(rG) and poly(rC). No structure of an AXH complex with RNA or DNA is ...
... This preference corresponds to the same specificity observed for the full-length protein (Yue et al., 2001). HBP1_AXH (de Chiara et al., 2003; Yue et al., 2001) binds poly(rU) and poly(rA). Weaker or no binding was observed for poly(rG) and poly(rC). No structure of an AXH complex with RNA or DNA is ...
Detection of Protein Coding Sequences Using a Mixture Model for
... 1999) and PROSITE (Hofmann et al., 1999; Bucher and Bairoch, 1994) databases, they are not speci c for particular types of proteins; rather, they transcend protein family boundaries. Because these sequence patterns are recurring features of protein sequences on a length scale neglected by most curr ...
... 1999) and PROSITE (Hofmann et al., 1999; Bucher and Bairoch, 1994) databases, they are not speci c for particular types of proteins; rather, they transcend protein family boundaries. Because these sequence patterns are recurring features of protein sequences on a length scale neglected by most curr ...
RNA-seq presentation
... – De-novo assemble into contigs first. – Then use reference to extend contigs into longer transcripts. – Small errors in the reference genome don’t get propagated into the new assembly. ...
... – De-novo assemble into contigs first. – Then use reference to extend contigs into longer transcripts. – Small errors in the reference genome don’t get propagated into the new assembly. ...
Slide 1
... monogenic diseases (e.g., cystic fibrosis) nsSNPs are frequent (>1%) and can modify risks of major common (multigenic, complex) diseases (e.g., cancer, cardiovascular disease, mental illness, autoimmune states, diabetes) In some cases, however, it is difficult to make a distinction ...
... monogenic diseases (e.g., cystic fibrosis) nsSNPs are frequent (>1%) and can modify risks of major common (multigenic, complex) diseases (e.g., cancer, cardiovascular disease, mental illness, autoimmune states, diabetes) In some cases, however, it is difficult to make a distinction ...
Lab 9: Web Applications for Gene Family Evolution
... than the others. Also note that this sequence is four base pairs longer than the others. We could simply leave the sequences as they are, but we might be able to do some additional aligning to get us closer to the true phylogenetic signal. One thing we might do is use ClustalW through Jalview to ali ...
... than the others. Also note that this sequence is four base pairs longer than the others. We could simply leave the sequences as they are, but we might be able to do some additional aligning to get us closer to the true phylogenetic signal. One thing we might do is use ClustalW through Jalview to ali ...
Bioinformatics
... length, thus cladograms show common ancestry, but do not indicate the amount of evolutionary “time” separating taxa. • It can align either nucleotide or protein sequences. In the case of nucleotide sequences, it will align them as they are input – the program does not provide the option of specifyin ...
... length, thus cladograms show common ancestry, but do not indicate the amount of evolutionary “time” separating taxa. • It can align either nucleotide or protein sequences. In the case of nucleotide sequences, it will align them as they are input – the program does not provide the option of specifyin ...
Introduction to BLAST ppt
... S. Needleman and C. Wunsch (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins, J. Molecular Biology, 48:443-453. D. Hirschberg (1975). A linear space algorithm for computing maximal common subsequences. Communications of the ACM, 18(6):341-3 ...
... S. Needleman and C. Wunsch (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins, J. Molecular Biology, 48:443-453. D. Hirschberg (1975). A linear space algorithm for computing maximal common subsequences. Communications of the ACM, 18(6):341-3 ...
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 ...
Introduction to BLAST
... S. Needleman and C. Wunsch (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins, J. Molecular Biology, 48:443-453. D. Hirschberg (1975). A linear space algorithm for computing maximal common subsequences. Communications of the ACM, 18(6):341-3 ...
... S. Needleman and C. Wunsch (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins, J. Molecular Biology, 48:443-453. D. Hirschberg (1975). A linear space algorithm for computing maximal common subsequences. Communications of the ACM, 18(6):341-3 ...
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 ...
Text S1.
... with this position now occupied by sponges (BS=80%), and Placozoa are now sistergroup to Bilateria (BS=61%). In other words, merely using a close outgroup is enough to make the analysis of the Schierwater et al. dataset congruent with the topology of Philippe et al. [4]. It is noteworthy that the se ...
... with this position now occupied by sponges (BS=80%), and Placozoa are now sistergroup to Bilateria (BS=61%). In other words, merely using a close outgroup is enough to make the analysis of the Schierwater et al. dataset congruent with the topology of Philippe et al. [4]. It is noteworthy that the se ...
Sequence editing and analysis PDF
... read and CO1F is the forward read (usually 5’ – 3’) of the coxI gene region. We can ignore the next two pieces of information (032_A16) – they are for the sequencing laboratory -- and .ab1 indicates it comes from the automated ABI sequencer. 2. Highlight both sequences (click and hold the shift key, ...
... read and CO1F is the forward read (usually 5’ – 3’) of the coxI gene region. We can ignore the next two pieces of information (032_A16) – they are for the sequencing laboratory -- and .ab1 indicates it comes from the automated ABI sequencer. 2. Highlight both sequences (click and hold the shift key, ...
Chapter 2 SEQUENCE ALIGNMENT
... between C and T) generally occur more frequently than transversions (When A or G is replaced by C or T). This suggests that we should not treat transitional differences and transversional differences with the same mismatch score. Instead, transitions should be penalized less than transversions. Seco ...
... between C and T) generally occur more frequently than transversions (When A or G is replaced by C or T). This suggests that we should not treat transitional differences and transversional differences with the same mismatch score. Instead, transitions should be penalized less than transversions. Seco ...
Identification of Short Motifs for Comparing Biological Sequences
... propose another way to measure the correctness. Clustering the species based on the resulting distances would provide a way to evaluate the correctness of these results. The clustering would be done using bi-clustering algorithms for phylogeny. Using the resulting trees of the phylogeny would be a g ...
... propose another way to measure the correctness. Clustering the species based on the resulting distances would provide a way to evaluate the correctness of these results. The clustering would be done using bi-clustering algorithms for phylogeny. Using the resulting trees of the phylogeny would be a g ...
Microbial Community Analysis
... community using sequences of 16S rRNA amplicons cloned to E. coli. But the number of clones available for analysis is limited due the high cost of this method. This disadvantage of the clone library method, which uses Sanger DNA sequencing, can be overcome by the use of pyrosequencing (a type of NGS ...
... community using sequences of 16S rRNA amplicons cloned to E. coli. But the number of clones available for analysis is limited due the high cost of this method. This disadvantage of the clone library method, which uses Sanger DNA sequencing, can be overcome by the use of pyrosequencing (a type of NGS ...
Comparison of DNA Sequences with Protein Sequences
... execution time required to compute an optimal alignment. The FASTX approach, which models only frameshift errors at codon boundaries, is similar to techniques developed by Guan and Uberbacher (1996), although judging by their published description, our algorithm (Zhang et al., 1997) is more efficien ...
... execution time required to compute an optimal alignment. The FASTX approach, which models only frameshift errors at codon boundaries, is similar to techniques developed by Guan and Uberbacher (1996), although judging by their published description, our algorithm (Zhang et al., 1997) is more efficien ...
Trees from proteins I
... • Produced a phylogenetic trees for every family and used maximum likelihood to estimate the relative rate values in the rate matrix (overall lnL over 182 different trees) – Better fit of the model with most data (significant improvement of the lnL of a tree when compared to PAM or JTT matrices) ...
... • Produced a phylogenetic trees for every family and used maximum likelihood to estimate the relative rate values in the rate matrix (overall lnL over 182 different trees) – Better fit of the model with most data (significant improvement of the lnL of a tree when compared to PAM or JTT matrices) ...
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.