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 ...
Mgr. Martina Višňovská Alignments on Sequences with Internal
... similarities, statistical significance (P -value) of the alignment is estimated. The matches with small enough P -value are then considered to be the relevant similarities. In this context, P -value is the probability that an alignment with a given score or higher would occur by chance in a comparis ...
... similarities, statistical significance (P -value) of the alignment is estimated. The matches with small enough P -value are then considered to be the relevant similarities. In this context, P -value is the probability that an alignment with a given score or higher would occur by chance in a comparis ...
Integration of tools - BioBIKE Portal
... similar to the rII protein of bacteriophage T4 (if you’ve never heard of this protein, no matter). Specifically: - Find such proteins ...
... similar to the rII protein of bacteriophage T4 (if you’ve never heard of this protein, no matter). Specifically: - Find such proteins ...
Star Method for MSA and Its Parallelization
... To facilitate vectorization and ensure that memory access to H is coalesced, elements of H is arranged such that each anti-diagonal is placed one another, rather than using the more conventional row- or column-major. Using this arrangement, each thread in a block can directly reads and writes consec ...
... To facilitate vectorization and ensure that memory access to H is coalesced, elements of H is arranged such that each anti-diagonal is placed one another, rather than using the more conventional row- or column-major. Using this arrangement, each thread in a block can directly reads and writes consec ...
Document
... signatures of motifs and domains Prosite consists of annotated sites/motifs/signatures/fingerprints Given an uncharacterized translated protein sequence, prosite tries to predict which motifs and domains make up the protein and thus identify the family to which it belongs ...
... signatures of motifs and domains Prosite consists of annotated sites/motifs/signatures/fingerprints Given an uncharacterized translated protein sequence, prosite tries to predict which motifs and domains make up the protein and thus identify the family to which it belongs ...
Evolution of genes, evolution of species: the case of aminoacyl
... 1993). Conversely, it is only recently that the archaebacterial LysRS’s from Methanococcus maripaludis, Methanobacterium thermoautotrophicum, and Methanococcus jannaschii (but not that from Sulfolobus solfataricus) and the LysRS from the spirochete Borrelia burgdorferi have been shown to be radicall ...
... 1993). Conversely, it is only recently that the archaebacterial LysRS’s from Methanococcus maripaludis, Methanobacterium thermoautotrophicum, and Methanococcus jannaschii (but not that from Sulfolobus solfataricus) and the LysRS from the spirochete Borrelia burgdorferi have been shown to be radicall ...
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 ...
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 ...
Phylogenetic Motif Detection by Expectation
... sequences (from all genes and all species) and calculated the negative log ratio of the MEME e-values for the two motifs (figure 2, heavy trace). MEME treats all the sequences independently, and continues to assign the polyT matrix a lower e-value over all the evolutionary distances. At least for th ...
... sequences (from all genes and all species) and calculated the negative log ratio of the MEME e-values for the two motifs (figure 2, heavy trace). MEME treats all the sequences independently, and continues to assign the polyT matrix a lower e-value over all the evolutionary distances. At least for th ...
Guide for Bioinformatics Project Module 3 - SGD-Wiki
... probable that they fold in a similar manner. Therefore, the structure corresponding to the PDB BLAST hit predicts how your query gene product is likely to fold. Record the PDB Code, Name, Lengt ...
... probable that they fold in a similar manner. Therefore, the structure corresponding to the PDB BLAST hit predicts how your query gene product is likely to fold. Record the PDB Code, Name, Lengt ...
Text S1, DOCX file, 0.03 MB
... using the gappyout flag (12) and the best-fit model for protein evolution for each alignment was determined using prottest (13), which indicated the LG + F model (14) was the best fit for 15 of the 16 genes using both the Aikake and Bayesian information criteria. The trimmed alignments were concaten ...
... using the gappyout flag (12) and the best-fit model for protein evolution for each alignment was determined using prottest (13), which indicated the LG + F model (14) was the best fit for 15 of the 16 genes using both the Aikake and Bayesian information criteria. The trimmed alignments were concaten ...
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. ...
comparing dna sequences to determine evolutionary relationships
... Before you can compare sequences, you have to “align” them, which means lining up the sequences and sliding them past one another until the best matching pattern is found. Alignment allows you to examine differences between related sequences; such differences reflect evolutionary relationships. ...
... Before you can compare sequences, you have to “align” them, which means lining up the sequences and sliding them past one another until the best matching pattern is found. Alignment allows you to examine differences between related sequences; such differences reflect evolutionary relationships. ...
Geneious Sequence Classifier User Manual
... database sequences. There is a trade-off between how fast the search runs versus how sensitive it is to finding distantly related matches. A higher sensitivity will align queries that are more distantly related to the database, so if you suspect your query sequence may be only distantly related to y ...
... database sequences. There is a trade-off between how fast the search runs versus how sensitive it is to finding distantly related matches. A higher sensitivity will align queries that are more distantly related to the database, so if you suspect your query sequence may be only distantly related to y ...
Identification of Prokaryotic Small Proteins using a Comparative
... that measured the ratio of nucleotide substitution rates between non-synonymous and synonymous mutation sites [16]. This method is based on a prior observation that among a set of closely related protein coding sequences, divergence at synonymous sites is greater than at non-synonymous sites [22, 11 ...
... that measured the ratio of nucleotide substitution rates between non-synonymous and synonymous mutation sites [16]. This method is based on a prior observation that among a set of closely related protein coding sequences, divergence at synonymous sites is greater than at non-synonymous sites [22, 11 ...
1 - BioMed Central
... Pairwise comparisons of chicken and zebra finch genes: A set of 3,653 chicken and zebra finch CDS pairwise alignments were examined to identify candidate genes potentially subject to directional selection. Ten candidate genes were observed with ω > 0.5 where the variable model was significantly favo ...
... Pairwise comparisons of chicken and zebra finch genes: A set of 3,653 chicken and zebra finch CDS pairwise alignments were examined to identify candidate genes potentially subject to directional selection. Ten candidate genes were observed with ω > 0.5 where the variable model was significantly favo ...
such as for example in pairwise distance methods
... RNA: rRNA often used for constructing species trees ...
... RNA: rRNA often used for constructing species trees ...
genetic diversity of american-type vaccine-derived prrs
... Materials and Methods In our facilities routine detection of PRRSV from diagnostic samples is performed by an ORF7 PRRS-PCR discriminating between the european and american genotype. Positive samples of american- type were subjected to full length ORF5 sequencing. The amino acid sequences of ORF5 we ...
... Materials and Methods In our facilities routine detection of PRRSV from diagnostic samples is performed by an ORF7 PRRS-PCR discriminating between the european and american genotype. Positive samples of american- type were subjected to full length ORF5 sequencing. The amino acid sequences of ORF5 we ...
Supplementary Material (doc 28K)
... 1,714, a reduction of 99.9%. This final set of patterns was smaller by 21.5% than the one in the CLL dataset although the number of sequences analyzed was almost twice as high (5,344 vs. 2,845). This was partly due to the fact that this set of sequences was a sum of several different entities. Furth ...
... 1,714, a reduction of 99.9%. This final set of patterns was smaller by 21.5% than the one in the CLL dataset although the number of sequences analyzed was almost twice as high (5,344 vs. 2,845). This was partly due to the fact that this set of sequences was a sum of several different entities. Furth ...
ADOPS - Automatic Detection Of Positively Selected Sites 1
... brucei genes [17], at the vertebrate skeletal muscle sodium channel gene [18], at the p53 gene [19], the fruitless gene in Anastrepha fruit flies [20], CC chemokine receptor proteins [21], or at the plant genes that are involved in gametophytic self-incompatibility specificity determination [22, 23, ...
... brucei genes [17], at the vertebrate skeletal muscle sodium channel gene [18], at the p53 gene [19], the fruitless gene in Anastrepha fruit flies [20], CC chemokine receptor proteins [21], or at the plant genes that are involved in gametophytic self-incompatibility specificity determination [22, 23, ...
Glossary - ChristopherKing.name
... genomic DNA contigs, mRNAs, proteins, and entire chromosomes. Accession numbers have the format of two letters, an underscore bar, and six digits. Example: NT_123456. Code: NT, NC, NG = genomic; NM = mRNA; NP = protein (for more of the two letter codes, see the NCBI site map). Sequence Manipulation ...
... genomic DNA contigs, mRNAs, proteins, and entire chromosomes. Accession numbers have the format of two letters, an underscore bar, and six digits. Example: NT_123456. Code: NT, NC, NG = genomic; NM = mRNA; NP = protein (for more of the two letter codes, see the NCBI site map). Sequence Manipulation ...
An Introduction to Hidden Markov Models for Biological Sequences
... 4.1 Introduction Very efficient programs for searching a text for a combination of words are available on many computers. The same methods can be used for searching for patterns in biological sequences, but often they fail. This is because biological ‘spelling’ is much more sloppy than English spel ...
... 4.1 Introduction Very efficient programs for searching a text for a combination of words are available on many computers. The same methods can be used for searching for patterns in biological sequences, but often they fail. This is because biological ‘spelling’ is much more sloppy than English spel ...
Convergent_Evolution_instructor_edited
... 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 will open a page that provides the amino acid sequence of the prestin protein from a particular species in a standard format, ...
... 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 will open a page that provides the amino acid sequence of the prestin protein from a particular species in a standard format, ...
Supplementary Methods Sampling and sequencing Five adult C
... Illumina reads were mapped to the contigs using BWA. Potential PCR duplicates (i.e., identical reads from the same individual) were removed. Contig coverage was calculated as the summed length of reads mapping to that contig divided by contig length. Contigs less covered than an average 2.5 X per in ...
... Illumina reads were mapped to the contigs using BWA. Potential PCR duplicates (i.e., identical reads from the same individual) were removed. Contig coverage was calculated as the summed length of reads mapping to that contig divided by contig length. Contigs less covered than an average 2.5 X per in ...
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.