Comparison of FIESTA and gadolinium-enhanced T1
... chromosome 22.23 There are reported cases of radiation induced AS in the literature, with Salvati et al. describing five cases with a latency of 20 years.24 The vestibular nerve (90%) is more commonly involved than the cochlear nerve (10%), and Stone et al. state that the inferior segment was more c ...
... chromosome 22.23 There are reported cases of radiation induced AS in the literature, with Salvati et al. describing five cases with a latency of 20 years.24 The vestibular nerve (90%) is more commonly involved than the cochlear nerve (10%), and Stone et al. state that the inferior segment was more c ...
Annotation Strategy Guide - GEP Community Server
... coding exon (1_3529_0) of Or13a on contig47 in D. mojavensis. According to the blastx track on the GEP UCSC Genome Browser, Or13a is oriented on the reverse strand in contig47. The CDS 1_3529_0 has a total length of 117 amino acids in D. melanogaster. Step 1: I performed a tblastn search with the CD ...
... coding exon (1_3529_0) of Or13a on contig47 in D. mojavensis. According to the blastx track on the GEP UCSC Genome Browser, Or13a is oriented on the reverse strand in contig47. The CDS 1_3529_0 has a total length of 117 amino acids in D. melanogaster. Step 1: I performed a tblastn search with the CD ...
Purification and amino acid sequence of a bacteriocins produced by
... FK22. Molecular weight of this fraction was 4331.70 Da. By amino acid sequence, this peptide was homology to Abp 118 beta produced by Lb. salivarius UCC118. In addition, Lb. salivarius UCC118 produced 2-peptide bacteriocin, which was Abp 118 alpha and beta. Based on the partial amino acid sequences ...
... FK22. Molecular weight of this fraction was 4331.70 Da. By amino acid sequence, this peptide was homology to Abp 118 beta produced by Lb. salivarius UCC118. In addition, Lb. salivarius UCC118 produced 2-peptide bacteriocin, which was Abp 118 alpha and beta. Based on the partial amino acid sequences ...
Co-evolving residues in membrane proteins
... perturbation-based methods such as SCA (Statistical Coupling Analysis) (Dekker et al., 2004; Lockless and Ranganathan, 1999; Suel et al., 2003) where co-evolution of residues is identified by the analysis of statistical coupling of amino acid distributions. Subalignments having a changed amino acid ...
... perturbation-based methods such as SCA (Statistical Coupling Analysis) (Dekker et al., 2004; Lockless and Ranganathan, 1999; Suel et al., 2003) where co-evolution of residues is identified by the analysis of statistical coupling of amino acid distributions. Subalignments having a changed amino acid ...
Sequence Note Complete 59 Long Terminal Repeat, nef,
... most probably not fold correctly or be directed to the membrane.16 All isolates with the exception of TV005, TV006, TV012, and TV013 as well as reference strain 96BW12-10 from Botswana have conserved GGXXS motifs in their myristoylation signals. It has been described that GSXXS mutations are possibl ...
... most probably not fold correctly or be directed to the membrane.16 All isolates with the exception of TV005, TV006, TV012, and TV013 as well as reference strain 96BW12-10 from Botswana have conserved GGXXS motifs in their myristoylation signals. It has been described that GSXXS mutations are possibl ...
Comparative sequence analysis of the long repeat regions and
... tations (see Fig. 1). One well characterized gene was recognized in R L, encoding the immediate early transcriptional regulatory protein IE 110 or ICP0; this gene is flanked by substantial sequences the roles of which were less well defined. Downstream of the IE110 gene is a region of some 3500 bp w ...
... tations (see Fig. 1). One well characterized gene was recognized in R L, encoding the immediate early transcriptional regulatory protein IE 110 or ICP0; this gene is flanked by substantial sequences the roles of which were less well defined. Downstream of the IE110 gene is a region of some 3500 bp w ...
PDF
... to first intron in rice, so our results are similar to those previously reported in Drosophila. In a comparison of two species of Drosophila (D. melanogaster and D. yakuba), Haddrill et al. [13] found that first introns evolve at similar rates to other introns. In rodents and mammals, however, it ha ...
... to first intron in rice, so our results are similar to those previously reported in Drosophila. In a comparison of two species of Drosophila (D. melanogaster and D. yakuba), Haddrill et al. [13] found that first introns evolve at similar rates to other introns. In rodents and mammals, however, it ha ...
BLAST Output Viewer Generator
... BLAST interface can be confusing when the BLAST output contains large number of matches. For example, when we use BLAST to align protein and mRNA sequences against the fosmid genomic sequences, it is often difficult to ascertain if the entire protein matched against the fosmid sequence and if certai ...
... BLAST interface can be confusing when the BLAST output contains large number of matches. For example, when we use BLAST to align protein and mRNA sequences against the fosmid genomic sequences, it is often difficult to ascertain if the entire protein matched against the fosmid sequence and if certai ...
GENtle, a free multi-purpose molecular biology tool
... information. This trend notwithstanding, general purpose software for these tasks often suffers from severe drawbacks. Free software exists, but is often hard to set up and operate for users on today’s point-and-click interfaces, and usually leads to the application of a patch-work of multiple, only ...
... information. This trend notwithstanding, general purpose software for these tasks often suffers from severe drawbacks. Free software exists, but is often hard to set up and operate for users on today’s point-and-click interfaces, and usually leads to the application of a patch-work of multiple, only ...
RNA-Seq Alignment v1.0 App Guide
... Arabidopsis thaliana Ensembl TAIR10 (Ensembl gene annotation) Bos taurus UCSC bosTau6 (RefSeq gene annotation) Caenorhabditis elegans UCSC ce10 (RefSeq gene annotation) Danio rerio UCSC danRer7 (RefSeq gene annotation) Drosophila melanogaster UCSC dm3 (RefSeq gene annotation) Gallus gallus UCSC galG ...
... Arabidopsis thaliana Ensembl TAIR10 (Ensembl gene annotation) Bos taurus UCSC bosTau6 (RefSeq gene annotation) Caenorhabditis elegans UCSC ce10 (RefSeq gene annotation) Danio rerio UCSC danRer7 (RefSeq gene annotation) Drosophila melanogaster UCSC dm3 (RefSeq gene annotation) Gallus gallus UCSC galG ...
Genomic Sequence Data - G3: Genes | Genomes | Genetics
... applied to the development of computational methods for de novo assembly of genomes using the type of data generated by these technologies: typically, shorter reads and/or higher error frequencies versus traditional Sanger sequencing1,2. The majority of that effort has focused on the assembly of in ...
... applied to the development of computational methods for de novo assembly of genomes using the type of data generated by these technologies: typically, shorter reads and/or higher error frequencies versus traditional Sanger sequencing1,2. The majority of that effort has focused on the assembly of in ...
Matthew Kwong - GEP Community Server
... Annotation projects involving multiple species of the same genus are important for understanding genomic evolution, adaptation, and conserved function. The Drosophila 12 Genomes Consortium paper titled, "Evolution of genes and genomes on the Drosophila phylogeny" demonstrates the wealth of knowledge ...
... Annotation projects involving multiple species of the same genus are important for understanding genomic evolution, adaptation, and conserved function. The Drosophila 12 Genomes Consortium paper titled, "Evolution of genes and genomes on the Drosophila phylogeny" demonstrates the wealth of knowledge ...
Sequence Heterogeneities Among 16s
... different but closely related genera (enterobacteria) and for different species or strains within a single genus (Escherichia or Salmonella), and finally how similar are the ribosomal operons within a single organism (Escherichia coli). These sequences have been analyzed by neighbor-joining, maximum ...
... different but closely related genera (enterobacteria) and for different species or strains within a single genus (Escherichia or Salmonella), and finally how similar are the ribosomal operons within a single organism (Escherichia coli). These sequences have been analyzed by neighbor-joining, maximum ...
Slide 1
... blastResult_direct_data: blast result file.[BLAST_report]. Use either this parameter or blastResult_url parameter as input but not both together. blastResult_url: url of the blast result. .[BLAST_report]. oldRefFile_direct_data: old blast result file..[BLAST_report]. Use either this parameter or old ...
... blastResult_direct_data: blast result file.[BLAST_report]. Use either this parameter or blastResult_url parameter as input but not both together. blastResult_url: url of the blast result. .[BLAST_report]. oldRefFile_direct_data: old blast result file..[BLAST_report]. Use either this parameter or old ...
Site specific insertion of a type I rDNA dement into a unique
... a type I insertion is shown in Figure 1. It is a 12.5Kb EcoRI fragment that is cleaved at eight sites by Hindlll. Two of the resulting Hindlll fragments, 8a/5 and 8a/6 are shown on the physical map. The 12.5Kb EcoRI fragment has been re-cloned into pBR322 and Figure 2 shows digests of this recombina ...
... a type I insertion is shown in Figure 1. It is a 12.5Kb EcoRI fragment that is cleaved at eight sites by Hindlll. Two of the resulting Hindlll fragments, 8a/5 and 8a/6 are shown on the physical map. The 12.5Kb EcoRI fragment has been re-cloned into pBR322 and Figure 2 shows digests of this recombina ...
Two groups of human herpesvirus 6 identified by sequence
... However, these viruses are distant relations: with the exception of the sequence around the conserved spliced gene (66% identity) (Efstathiou et al., 1988), little nucleotide sequence similarity exists that can be detected by Southern blot hybridization. A similar relationship is observed between va ...
... However, these viruses are distant relations: with the exception of the sequence around the conserved spliced gene (66% identity) (Efstathiou et al., 1988), little nucleotide sequence similarity exists that can be detected by Southern blot hybridization. A similar relationship is observed between va ...
software development and application in bioinformatics: single
... quality score assignment; Phrap is used for constructing assembly (Phrap uses input files and Phred’s outputs), and Consend for handling the ultimate output for a graphical visualization of the assembly and SNP calls [25]. For better accuracy in its calls, Polyphred relies on peaks analysis combined ...
... quality score assignment; Phrap is used for constructing assembly (Phrap uses input files and Phred’s outputs), and Consend for handling the ultimate output for a graphical visualization of the assembly and SNP calls [25]. For better accuracy in its calls, Polyphred relies on peaks analysis combined ...
巴西橡胶Pto类抗病同源序列的克隆与系统发育重建
... Abstract: The tomato Pto gene encodes a serine/threonine kinase (STK) whose molecular characterization has provided valuable insights into the disease resistance mechanism of tomato and it is considered as a promising candidate for engineering broad-spectrum pathogen resistance in this crop. In this ...
... Abstract: The tomato Pto gene encodes a serine/threonine kinase (STK) whose molecular characterization has provided valuable insights into the disease resistance mechanism of tomato and it is considered as a promising candidate for engineering broad-spectrum pathogen resistance in this crop. In this ...
Nomenclature for factors of the Dog Major
... sequenced, etc. We will also record the breed of dog in which the sequence was found. This data will not be made public at this time, however, as such information may cause assumptions to be made about the restriction of particular alleles to certain breeds. (This is in keeping with the policy of th ...
... sequenced, etc. We will also record the breed of dog in which the sequence was found. This data will not be made public at this time, however, as such information may cause assumptions to be made about the restriction of particular alleles to certain breeds. (This is in keeping with the policy of th ...
pdf
... A total of 92 DNA clones containing sequences identified as homologous with known nifH sequences were retrieved from seven of the nine depths from which clone libraries were made (Table 1). The cDNA clone libraries were made from five depths, and a total of 99 cDNA sequences were obtained (Table 1). ...
... A total of 92 DNA clones containing sequences identified as homologous with known nifH sequences were retrieved from seven of the nine depths from which clone libraries were made (Table 1). The cDNA clone libraries were made from five depths, and a total of 99 cDNA sequences were obtained (Table 1). ...
Arc Diagrams: Visualizing Structure in Strings
... auto-correlation matrix; in its simplest form, a string of n symbols a1a2…an is represented by an n x n image in which the pixel at coordinates (i,j) is colored black if ai=aj and white otherwise. This image often provides a good picture of the string’s structure, with repeated subsequences showing ...
... auto-correlation matrix; in its simplest form, a string of n symbols a1a2…an is represented by an n x n image in which the pixel at coordinates (i,j) is colored black if ai=aj and white otherwise. This image often provides a good picture of the string’s structure, with repeated subsequences showing ...
Analysis of expressed sequence tags from the Huperzia serrata leaf
... analysis (Fig. 2). When mapped against the cellular component GO terms, 283 unique sequences (40.4%) each were directly associated with ‘Cell’ and ‘Cell part’ functions, respectively. A total of 155 unique sequences (22.1%) were assigned to the ‘Macromolecular complex’ (Fig. 2A). In contrast, the ma ...
... analysis (Fig. 2). When mapped against the cellular component GO terms, 283 unique sequences (40.4%) each were directly associated with ‘Cell’ and ‘Cell part’ functions, respectively. A total of 155 unique sequences (22.1%) were assigned to the ‘Macromolecular complex’ (Fig. 2A). In contrast, the ma ...
wsp Gene Sequences from the Wolbachia of Filarial Nematodes
... The PCR products obtained with primers WSPintF and WSPintR from nematode Wolbachia were sequenced directly, and the sequences were aligned to the wsp gene available for arthropod Wolbachia. We also tried to align wsp to the gene sequences available for the major outer membrane proteins of Anaplasma, ...
... The PCR products obtained with primers WSPintF and WSPintR from nematode Wolbachia were sequenced directly, and the sequences were aligned to the wsp gene available for arthropod Wolbachia. We also tried to align wsp to the gene sequences available for the major outer membrane proteins of Anaplasma, ...
Lack of biological significance in the `linguistic features` of
... for example, 3) that natural DNA sequences, and especially noncoding DNAs, appear to have many statistical features in common with natural languages. In the original paper (2), Mantegna et al. performed certain mathematical investigations—called ‘linguistic tests’—on DNA sequences, which are related ...
... for example, 3) that natural DNA sequences, and especially noncoding DNAs, appear to have many statistical features in common with natural languages. In the original paper (2), Mantegna et al. performed certain mathematical investigations—called ‘linguistic tests’—on DNA sequences, which are related ...
Exploring Human Visual Pigments Copyright 2008, Gale Rhodes
... your search, in the colors that signify their BLAST scores, are located for you on the diagram. Notice that there are about 100 proteins (discovered so far, that is) that have 40% or more positives in alignment with red opsin. The opsins are members of the very large family of G protein-coupled rece ...
... your search, in the colors that signify their BLAST scores, are located for you on the diagram. Notice that there are about 100 proteins (discovered so far, that is) that have 40% or more positives in alignment with red opsin. The opsins are members of the very large family of G protein-coupled rece ...
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.