software development and application in bioinformatics: single
... This thesis incorporates two projects, one in assessing software availability and application in detecting SNPs for next generation sequencing, and the other in software engineering of a social networking environment for use in biomedical informatics. SNP Detection: The study on variations in DNA se ...
... This thesis incorporates two projects, one in assessing software availability and application in detecting SNPs for next generation sequencing, and the other in software engineering of a social networking environment for use in biomedical informatics. SNP Detection: The study on variations in DNA se ...
Biomart/ GENOME ALIGNMENT III
... aligning large genomic regions and subsequently sifting through massive amounts of data. In order to facilitate the discovery process without requiring biologists to download and install complex software, a number of web servers for alignment and analysis have been set up in recent years. These serv ...
... aligning large genomic regions and subsequently sifting through massive amounts of data. In order to facilitate the discovery process without requiring biologists to download and install complex software, a number of web servers for alignment and analysis have been set up in recent years. These serv ...
pdf
... using Big DyeTM terminator chemistry (Applied Biosystems, Carlsbad, CA). Sequences were edited using FINCHTV ver. 1.4.0 (Geospiza Inc.) and checked for identity using BLAST. Consensus nifH sequences (359 bp) were translated to amino acid (aa) sequences (108 aa after trimming the primer region) and a ...
... using Big DyeTM terminator chemistry (Applied Biosystems, Carlsbad, CA). Sequences were edited using FINCHTV ver. 1.4.0 (Geospiza Inc.) and checked for identity using BLAST. Consensus nifH sequences (359 bp) were translated to amino acid (aa) sequences (108 aa after trimming the primer region) and a ...
3 -2 -1 -2 -1 1 2 K
... Step 4: Selecting search parameters and formatting parameters Stand-alone BLAST BLAST algorithm uses local alignment search strategy BLAST algorithm parts: list, scan, extend BLAST algorithm: local alignment search statistics and E ...
... Step 4: Selecting search parameters and formatting parameters Stand-alone BLAST BLAST algorithm uses local alignment search strategy BLAST algorithm parts: list, scan, extend BLAST algorithm: local alignment search statistics and E ...
Origin and evolution of the slime molds (Mycetozoa)
... The Mycetozoa include the cellular (dictyostelid), acellular (myxogastrid), and protostelid slime molds. However, available molecular data are in disagreement on both the monophyly and phylogenetic position of the group. Ribosomal RNA trees show the myxogastrid and dictyostelid slime molds as unrela ...
... The Mycetozoa include the cellular (dictyostelid), acellular (myxogastrid), and protostelid slime molds. However, available molecular data are in disagreement on both the monophyly and phylogenetic position of the group. Ribosomal RNA trees show the myxogastrid and dictyostelid slime molds as unrela ...
Definitions for annotating CDS sequences
... that flank the relevant CDS that need to be analyzed at the nucleotide level, it is sufficient to indicate “N/A”. It is also worth noting that any sequences outside of the linker sequences will be masked out and not analyzed. 5’ Linker – any sequences upstream of the relevant CDS for which the user ...
... that flank the relevant CDS that need to be analyzed at the nucleotide level, it is sufficient to indicate “N/A”. It is also worth noting that any sequences outside of the linker sequences will be masked out and not analyzed. 5’ Linker – any sequences upstream of the relevant CDS for which the user ...
pdf
... (Perkin-Elmer). Cycle-sequencing products were precipitated according to the manufacturer’s instructions and sequenced on the ABI310 genetic analyzer (Perkin-Elmer). Ammonia monooxygenase PCR amplification and sequencing. Fragments of the amoA gene were PCR amplified from genomic DNA using the Amo18 ...
... (Perkin-Elmer). Cycle-sequencing products were precipitated according to the manufacturer’s instructions and sequenced on the ABI310 genetic analyzer (Perkin-Elmer). Ammonia monooxygenase PCR amplification and sequencing. Fragments of the amoA gene were PCR amplified from genomic DNA using the Amo18 ...
Matthew Kwong - GEP Community Server
... corresonding donor and acceptor sites have a phase that add up to three or zero. This is the way that the amino acid sequences are conserved from one exon to the next. There are often many possible candidates for donor sites (and sometimes acceptor sites as well). One considers all donor sites until ...
... corresonding donor and acceptor sites have a phase that add up to three or zero. This is the way that the amino acid sequences are conserved from one exon to the next. There are often many possible candidates for donor sites (and sometimes acceptor sites as well). One considers all donor sites until ...
A Plastid in the Making: Evidence for a Second
... Figure 1. a. Phylogenetic evidence for an independent cyanobacterial origin of the photosynthetic organelle of Paulinella chromatophora, significantly separated from the plastid lineage. The maximum-likelihood tree (GTR+I+G; I ¼ 0:2661; G ¼ 0:7513) was based on almost-complete rDNA operon sequences ...
... Figure 1. a. Phylogenetic evidence for an independent cyanobacterial origin of the photosynthetic organelle of Paulinella chromatophora, significantly separated from the plastid lineage. The maximum-likelihood tree (GTR+I+G; I ¼ 0:2661; G ¼ 0:7513) was based on almost-complete rDNA operon sequences ...
wsp Gene Sequences from the Wolbachia of Filarial Nematodes
... expected from the unreliability of the alignment, phylogenetic analysis showed arthropod and nematode wsp sequences closely related relative to the surface-protein genes of Anaplasma, Ehrlichia, and Cowdria. Because of the ambiguity of the alignment, for further phylogenetic analyses we did not incl ...
... expected from the unreliability of the alignment, phylogenetic analysis showed arthropod and nematode wsp sequences closely related relative to the surface-protein genes of Anaplasma, Ehrlichia, and Cowdria. Because of the ambiguity of the alignment, for further phylogenetic analyses we did not incl ...
A molecular method for assessing meiofauna diversity in marine
... Molecular techniques could be beneficial to pollution studies and monitoring programs wanting to incorporate meiofauna data by lowering the cost of sample processing as well as eliminating the need for taxonomic expertise. In one study Litvaitis, et al. (1994) used a fragment of the nuclear 28S rRN ...
... Molecular techniques could be beneficial to pollution studies and monitoring programs wanting to incorporate meiofauna data by lowering the cost of sample processing as well as eliminating the need for taxonomic expertise. In one study Litvaitis, et al. (1994) used a fragment of the nuclear 28S rRN ...
Exploring Important Biological Concepts Using Biology Workbench
... Genetic Code: Missense mutations may result in a chemically similar amino acid being inserted at that position in an amino acid chain. Mutations that result in the substitution of one amino acid for another are termed missense mutations. Due to the relationship among codons in the genetic code, many ...
... Genetic Code: Missense mutations may result in a chemically similar amino acid being inserted at that position in an amino acid chain. Mutations that result in the substitution of one amino acid for another are termed missense mutations. Due to the relationship among codons in the genetic code, many ...
Acanthamoeba mitochondrial 16S rDNA sequences: inferred
... observed elsewhere for nuclear Rns DNA [3]. The exceptions were several mT4 strains with identical mitochondrial 16S rDNA sequences, but different nuclear sequences. There were a total of seven rns sequences, each from 2-10 strains, in which all strains shared the same sequence. One was a set of thr ...
... observed elsewhere for nuclear Rns DNA [3]. The exceptions were several mT4 strains with identical mitochondrial 16S rDNA sequences, but different nuclear sequences. There were a total of seven rns sequences, each from 2-10 strains, in which all strains shared the same sequence. One was a set of thr ...
Causes, consequences and solutions of
... amounts of data with available efficient algorithms have made immense progress, but still many important nodes remain unresolved [15, 19]. This issue raises a critical question: why important nodes remain unresolved, and how do we overcome this problem. Molecular data are continuously accumulating a ...
... amounts of data with available efficient algorithms have made immense progress, but still many important nodes remain unresolved [15, 19]. This issue raises a critical question: why important nodes remain unresolved, and how do we overcome this problem. Molecular data are continuously accumulating a ...
Multifractal characterisation of length sequences of coding and
... One can study the DNA sequences in detail by considering the order in which four kinds of nucleotides of DNA are assembled, namely adenine (a), cytosine (c), guanine (g), and thymine (t). There has been considerable interest in the 3nding of long-range correlation (LRC) in DNA sequences at this leve ...
... One can study the DNA sequences in detail by considering the order in which four kinds of nucleotides of DNA are assembled, namely adenine (a), cytosine (c), guanine (g), and thymine (t). There has been considerable interest in the 3nding of long-range correlation (LRC) in DNA sequences at this leve ...
as a PDF - Idiap Publications
... are generally classified following their degree of dependence on the pronounced text: text-dependent, text-prompted, and text-independent systems. Beside this classification, it is classically observed that the speaker recognition performance generally increases when introducing more knowledge about ...
... are generally classified following their degree of dependence on the pronounced text: text-dependent, text-prompted, and text-independent systems. Beside this classification, it is classically observed that the speaker recognition performance generally increases when introducing more knowledge about ...
An rpoB signature sequence provides unique resolution for the
... deletion) was noticed in the rpoB sequences of Nostocaceae, but was not discussed further (Rajaniemi et al., 2005). Indels have been used as phylogenetic characters to assess evolutionary relationships among many bacterial and archaeal phyla (Gupta, 1997, 1998) and recently among cyanobacterial taxa ...
... deletion) was noticed in the rpoB sequences of Nostocaceae, but was not discussed further (Rajaniemi et al., 2005). Indels have been used as phylogenetic characters to assess evolutionary relationships among many bacterial and archaeal phyla (Gupta, 1997, 1998) and recently among cyanobacterial taxa ...
RNA-Seq Alignment v1.0 App Guide
... Spliced Transcripts Alignment to a Reference (STAR) is a fast RNA-seq read mapper, with support for splice-junction and fusion read detection. STAR aligns reads by finding the Maximal Mappable Prefix (MMP) hits between reads (or read pairs) and the genome, using a Suffix Array index. Different parts ...
... Spliced Transcripts Alignment to a Reference (STAR) is a fast RNA-seq read mapper, with support for splice-junction and fusion read detection. STAR aligns reads by finding the Maximal Mappable Prefix (MMP) hits between reads (or read pairs) and the genome, using a Suffix Array index. Different parts ...
A large scale analysis of resistance gene
... A. thaliana for resistance to Pseudomonas syringae (gi 15221252), R-gene Mi-1 against nematodes and aphids from Lycopersicon esculentum (gi 7489037) and gene Rpp 8 of A. thaliana (gi 17064876). The sequence of primer RNBS-D-rev was kindly provided by Nevin Young. Primer LM638 was developed by Kanazi ...
... A. thaliana for resistance to Pseudomonas syringae (gi 15221252), R-gene Mi-1 against nematodes and aphids from Lycopersicon esculentum (gi 7489037) and gene Rpp 8 of A. thaliana (gi 17064876). The sequence of primer RNBS-D-rev was kindly provided by Nevin Young. Primer LM638 was developed by Kanazi ...
Molecular evidence for the existence of additional members of the
... from six patients during surgical treatment of their abdominal aneurysms. DNA was isolated from three specimens taken from different locations of the aneurysm of each patient using a PCR-inhibitor-free procedure as described previously (Meijer et al., 1998). Design of primers and probes. The 16s rRN ...
... from six patients during surgical treatment of their abdominal aneurysms. DNA was isolated from three specimens taken from different locations of the aneurysm of each patient using a PCR-inhibitor-free procedure as described previously (Meijer et al., 1998). Design of primers and probes. The 16s rRN ...
what is alignment? - UWI St. Augustine
... Significance of local sequence alignment •In global alignment, an attempt is made to align the entire sequences, as many characters as possible. • In local alignment, stretches of sequence with the highest density of matches are given the highest priority, •generating one or more islands of matches ...
... Significance of local sequence alignment •In global alignment, an attempt is made to align the entire sequences, as many characters as possible. • In local alignment, stretches of sequence with the highest density of matches are given the highest priority, •generating one or more islands of matches ...
Homologous and Nonhomologous Rearrangements: Interactions
... the processes closest to m (for which the highest efficiency, h, is reached). Thus, various types of proteins can co-exist, from highly efficient and specialized ones (small w, high h) to polyvalent but poorly efficient ones (large w, low h). In this framework, each protein’s primary sequence is dec ...
... the processes closest to m (for which the highest efficiency, h, is reached). Thus, various types of proteins can co-exist, from highly efficient and specialized ones (small w, high h) to polyvalent but poorly efficient ones (large w, low h). In this framework, each protein’s primary sequence is dec ...
BLSSpeller: exhaustive comparative discovery of
... collection of binding sites. The algorithm can be run in both alignment-free or alignment-based mode. In case of alignment-free discovery, the conservation of a motif is scored irrespective of its orientation or position within a promoter sequence. This relaxed definition of conservation was previou ...
... collection of binding sites. The algorithm can be run in both alignment-free or alignment-based mode. In case of alignment-free discovery, the conservation of a motif is scored irrespective of its orientation or position within a promoter sequence. This relaxed definition of conservation was previou ...
Consensus Clustering for Binning Metagenome Sequences
... In this paper we present a model based on consensus of different clustering models by the combination of different distances measures. The difference in the models are referred to the data use to train them. The data are reconstructed using different lengths of sequences. The proposed method is appl ...
... In this paper we present a model based on consensus of different clustering models by the combination of different distances measures. The difference in the models are referred to the data use to train them. The data are reconstructed using different lengths of sequences. The proposed method is appl ...
A method for fast database search for all k-nucleotide repeats
... tandem repeat. In the example above, we nd CTT repeated at an interval of 7 and conclude that CTTGCA could be a tandem repeat period. Note we are not looking speci cally for CTT , only for any 3 base string that repeats at an interval of 7. A pattern found by this method we denote a suspicious patt ...
... tandem repeat. In the example above, we nd CTT repeated at an interval of 7 and conclude that CTTGCA could be a tandem repeat period. Note we are not looking speci cally for CTT , only for any 3 base string that repeats at an interval of 7. A pattern found by this method we denote a suspicious patt ...
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.