Additional file 1
... 1、 The protein sequence of bh2b may be queried against transcription factor database of Jaspar[3] with blastp to gather information on likely DNA binding sites of bh2b, which is based on the PWMs of transcription factors that are similar to bh2b. The blastp result shows that bh2b is similar with tra ...
... 1、 The protein sequence of bh2b may be queried against transcription factor database of Jaspar[3] with blastp to gather information on likely DNA binding sites of bh2b, which is based on the PWMs of transcription factors that are similar to bh2b. The blastp result shows that bh2b is similar with tra ...
Fragaria multicipita - DigitalCommons@University of Nebraska
... primed by primer pair P1/P7 but from only rrnA in PCR primed by primer pair R16mF2/R16mR1. Preferential amplification of DNA from operon rrnA was explained by base mismatches between the R16mF2/R16mR1 primers and primer annealing sites in rrnB. The results revealed potential for classification of a ...
... primed by primer pair P1/P7 but from only rrnA in PCR primed by primer pair R16mF2/R16mR1. Preferential amplification of DNA from operon rrnA was explained by base mismatches between the R16mF2/R16mR1 primers and primer annealing sites in rrnB. The results revealed potential for classification of a ...
Rfam Documentation
... curator. As a result, attempts to obtain the same structure using the same prediction method, may not return exactly the same structure as shown on the Rfam SEED alignment. We usually indicate where the a structure has been manually edited. What is your definition of an RNA family? We will group seq ...
... curator. As a result, attempts to obtain the same structure using the same prediction method, may not return exactly the same structure as shown on the Rfam SEED alignment. We usually indicate where the a structure has been manually edited. What is your definition of an RNA family? We will group seq ...
Computational Definition of
... confounding presence of protein coding information was to restrict our search to non-proteincoding exons. In more than 40% of all human genes protein synthesis is initiated in an exon other than the first (Davuluri et al. 2001). By examining a database of unrelated human genes, 9% were found in whic ...
... confounding presence of protein coding information was to restrict our search to non-proteincoding exons. In more than 40% of all human genes protein synthesis is initiated in an exon other than the first (Davuluri et al. 2001). By examining a database of unrelated human genes, 9% were found in whic ...
Selecting Degenerate Multiplex PCR Primers
... the same, with the addition of additional sequence fragments. This observation permits us to employ a strategy which ignores degenerate primers with high degeneracy, in order to speed up the algorithm. Therefore, the search is restricted only to the primers with the lowest degeneracy. In this algori ...
... the same, with the addition of additional sequence fragments. This observation permits us to employ a strategy which ignores degenerate primers with high degeneracy, in order to speed up the algorithm. Therefore, the search is restricted only to the primers with the lowest degeneracy. In this algori ...
Rapid Diversification of RNase A Superfamily Ribonucleases from
... PCR II TA cloning vector (Invitrogen, San Diego, CA) and multiple clones were sequenced as described (Zhang et al. 2000). To avoid confounding results from PCR-induced mutation (estimated at 1 nucleotide in 1000 to 1 in 10,000 under these conditions), each sequence was isolated at least twice from i ...
... PCR II TA cloning vector (Invitrogen, San Diego, CA) and multiple clones were sequenced as described (Zhang et al. 2000). To avoid confounding results from PCR-induced mutation (estimated at 1 nucleotide in 1000 to 1 in 10,000 under these conditions), each sequence was isolated at least twice from i ...
Natural rules for Arabidopsis thaliana
... between up- and down-stream flank regions. The analysis showed the same results in both 5’ and 3’ splicing sites with the number of U in intron flank region larger than in exon flank region. This result was reversed for A, G, and C (Figure 2). Statistical analysis showed that there were significant ...
... between up- and down-stream flank regions. The analysis showed the same results in both 5’ and 3’ splicing sites with the number of U in intron flank region larger than in exon flank region. This result was reversed for A, G, and C (Figure 2). Statistical analysis showed that there were significant ...
Unipro UGENE Manual
... You're going to use only basic UGENE features and don't want to waste Internet traffic You have limited disk space Use the NGS package, if: You're going to analyze ChIP-Seq data with the Cistrome pipeline Explanation of the tip above: Some tools are embedded into UGENE as external. To be launched fr ...
... You're going to use only basic UGENE features and don't want to waste Internet traffic You have limited disk space Use the NGS package, if: You're going to analyze ChIP-Seq data with the Cistrome pipeline Explanation of the tip above: Some tools are embedded into UGENE as external. To be launched fr ...
Unipro UGENE Manual
... You're going to use only basic UGENE features and don't want to waste Internet traffic You have limited disk space Use the NGS package, if: You're going to analyze ChIP-Seq data with the Cistrome pipeline Explanation of the tip above: Some tools are embedded into UGENE as external. To be launched fr ...
... You're going to use only basic UGENE features and don't want to waste Internet traffic You have limited disk space Use the NGS package, if: You're going to analyze ChIP-Seq data with the Cistrome pipeline Explanation of the tip above: Some tools are embedded into UGENE as external. To be launched fr ...
Partial report - GEP Community Server
... Note: In some cases, the reconciled gene models (available under "Genes and Gene Prediction Tracks" this "Reconciled Gene GEP UCSC Genome Browser) might incorrect Complete report form for Models" each geneoninthe your project. Copy and paste this form tobe create as because of misannotations or bec ...
... Note: In some cases, the reconciled gene models (available under "Genes and Gene Prediction Tracks" this "Reconciled Gene GEP UCSC Genome Browser) might incorrect Complete report form for Models" each geneoninthe your project. Copy and paste this form tobe create as because of misannotations or bec ...
Understanding Reads in RNA-Seq Analysis
... they mapped to two different transcript or different chromosome, they are not compatible with a transcript. Reads that are partially mapped exon reads, intronic reads, intergenic reads are incompatible with any transcript. Incompatible reads do not contribute to gene or transcript level read counts. ...
... they mapped to two different transcript or different chromosome, they are not compatible with a transcript. Reads that are partially mapped exon reads, intronic reads, intergenic reads are incompatible with any transcript. Incompatible reads do not contribute to gene or transcript level read counts. ...
Comparative sequence analysis of the long repeat regions and
... Sequences were compiled using the program set of Staden (1982). Regions presenting problem sequences were resolved using electrophoresis in a 6% polyacrylamidegel containing 9 M-urea, with a water jacket maintained at approximately 80 to 85 °C. Some use was also made of Taq DNA polymerase (Promega) ...
... Sequences were compiled using the program set of Staden (1982). Regions presenting problem sequences were resolved using electrophoresis in a 6% polyacrylamidegel containing 9 M-urea, with a water jacket maintained at approximately 80 to 85 °C. Some use was also made of Taq DNA polymerase (Promega) ...
METADOMAIN: A PROFILE HMM-BASED PROTEIN DOMAIN
... probable state path in the model. Unlike HMMER, MetaDomain directly aligns a DNA sequence to a profile HMM. To do so, we implicitly align translated peptides under different reading frames with a profile HMM. Let π be a state path in a profile HMM M and let x be a query DNA sequence. The Viterbi algorit ...
... probable state path in the model. Unlike HMMER, MetaDomain directly aligns a DNA sequence to a profile HMM. To do so, we implicitly align translated peptides under different reading frames with a profile HMM. Let π be a state path in a profile HMM M and let x be a query DNA sequence. The Viterbi algorit ...
BLAST Output Viewer Generator
... While the graphical diagram generated by the web-based NCBI BLAST interface provide us with a general overview of the locations of the BLAST hits relative to our query sequence, we often need to investigate individual BLAST hits and examine their alignments in detail during the annotation process. I ...
... While the graphical diagram generated by the web-based NCBI BLAST interface provide us with a general overview of the locations of the BLAST hits relative to our query sequence, we often need to investigate individual BLAST hits and examine their alignments in detail during the annotation process. I ...
Co-evolving residues in membrane proteins
... changes were described by analyzing individual families having a solved structure (Altschuh et al., 1987, 1988). Amino acid contacts were initially thought to be primary spots of these compensatory processes, making the detection of sequence positions with correlated mutational behavior an interesti ...
... changes were described by analyzing individual families having a solved structure (Altschuh et al., 1987, 1988). Amino acid contacts were initially thought to be primary spots of these compensatory processes, making the detection of sequence positions with correlated mutational behavior an interesti ...
Annotation Strategy Guide - GEP Community Server
... (3): internal exons are highly conserved, flanking exons show little conservation, (4) low conservation in all exons, (5): very low conservation with flanking ends barely conserved Exons found on adjacent contigs: This example will demonstrate the step-by-step strategy for annotating the first cod ...
... (3): internal exons are highly conserved, flanking exons show little conservation, (4) low conservation in all exons, (5): very low conservation with flanking ends barely conserved Exons found on adjacent contigs: This example will demonstrate the step-by-step strategy for annotating the first cod ...
A Landform-based Approach for the
... physically interact with the World, and particularly with geographical systems. Influence of experientialism in geography and spatial cognition has already been discussed (e.g., [2][16][8]). It is claimed that the human perception of space lays on categories which are derived from the physical natur ...
... physically interact with the World, and particularly with geographical systems. Influence of experientialism in geography and spatial cognition has already been discussed (e.g., [2][16][8]). It is claimed that the human perception of space lays on categories which are derived from the physical natur ...
Action Classification Using Sequence Alignment and Shape Context and Eraldo Ribeiro
... of LCSS, the maximum number in the similarity table is the number of the similar points between the sequences. We assume that ε equals mean(D), where D is the matrix that contains the cost of shape context when comparing ...
... of LCSS, the maximum number in the similarity table is the number of the similar points between the sequences. We assume that ε equals mean(D), where D is the matrix that contains the cost of shape context when comparing ...
Genomic Sequence Data - G3: Genes | Genomes | Genetics
... metagenomic data that also includes host sequence and, commonly, non-pathogenic commensal microflora. Viral DNA or RNA typically makes up only a tiny fraction of the total nucleic acid in such samples, and while the small size of many viral genomes results in high genome coverage even given a small ...
... metagenomic data that also includes host sequence and, commonly, non-pathogenic commensal microflora. Viral DNA or RNA typically makes up only a tiny fraction of the total nucleic acid in such samples, and while the small size of many viral genomes results in high genome coverage even given a small ...
What`s new - JSI medical systems
... Ignore coverage: If the percentage coverage of a base is below this value the mutation will not be listed in the Variation/Mutation table. Therefore all base changed with a coverage below this value are regarded as likely basecalling errors. If the percentage coverage of a base is between the Ignore ...
... Ignore coverage: If the percentage coverage of a base is below this value the mutation will not be listed in the Variation/Mutation table. Therefore all base changed with a coverage below this value are regarded as likely basecalling errors. If the percentage coverage of a base is between the Ignore ...
PDF
... This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. ...
... This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. ...
WOMBO2011-09-Puri-et..
... ontology alignment using contextual information. • BLOOMS can be extended to utilize datasource of choice such as UMLS. • To the best of our knowledge, BLOOMS is the only system which utilizes contextual information present in ontology and Wikipedia category hierarchy for ontology matching. • BLOOMS ...
... ontology alignment using contextual information. • BLOOMS can be extended to utilize datasource of choice such as UMLS. • To the best of our knowledge, BLOOMS is the only system which utilizes contextual information present in ontology and Wikipedia category hierarchy for ontology matching. • BLOOMS ...
Analysis of expressed sequence tags from the Huperzia serrata leaf
... broad catalytic promiscuity, producing various aromatic ...
... broad catalytic promiscuity, producing various aromatic ...
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.