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Topic: Sequence analysis

Related Topics

Sequence alignment

Sequence database

Repeated Sequences

Sequence motif

Blast

Bioinformatics

Sequencing

Protein motif

Genetic code

Hidden Markov model

Markov process

Gene regulatory network

Genetic programming

Medical computer science

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	A high-throughput distributed DNA sequence analysis and database system
		With such numbers, the sequence analysis portions of the pipeline, such as similarity searching, could not keep up with the growth of the database if the analyses were performed on a single processor.
		The sequence analysis pipeline consists of an ordered set of processing stages, each of which does some well-understood operation on its input data, and produces output data that may be used by some subsequent stage.
		The sequences, their meta-data, and the results of their analyses, as well as some tables that are used to administer the pipeline, are all stored in a Sybase relational database.
	www.research.ibm.com /journal/sj/402/inman.html (7714 words)

	Sequence analysis - Wikipedia, the free encyclopedia
		The term "sequence analysis" in biology implies subjecting a DNA or peptide sequence to sequence alignment, sequence databases, repeated sequence searches, or other bioinformatics methods on a computer.
		Sequence analysis in molecular biology and bioinformatics is an automated, computer-based examination of characteristical fragments, e.g.
		In chemistry, sequence analysis comprises techniques used to determine the sequence of a polymer formed of several monomers.
	en.wikipedia.org /wiki/Sequence_analysis (140 words)

	oreilly.com -- Online Catalog: Sequence Analysis in a Nutshell: A Guide to Tools
		Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases pulls together all of the vital information about the most commonly used databases, analytical tools, and tables used in sequence analysis.
		Gene sequence data is the most abundant type of data available, and if you're interested in analyzing it, you'll find a wealth of computational methods and tools to help you.
		The basic idea behind sequence analysis is the classification of DNA or protein sequences in terms of other known DNA or protein sequences.
	www.oreilly.com /catalog/seqanalyian (2066 words)

	GeneQuiz - A System for Sequence Analysis (Site not responding. Last check: 2007-09-11)
		GeneQuiz is an integrated system for large-scale biological sequence analysis, that goes from a protein sequence to a biochemical function, using a variety of search and analysis methods and up-to-date protein and DNA databases.
		As genome sequence data is being produced at an accelerating pace, there is a need for faster and more reliable methods of large-scale sequence analysis.
		Large-scale sequence analysis differs from traditional practices in two basic respects: first, computational efficiency using fast algorithms and certain heuristics is essential; second, knowledge support for expert users is becoming crucial, as the emerging gene and protein families from genome projects extend beyond the areas of expertise of a single individual.
	jura.ebi.ac.uk:8765 /ext-genequiz/genequiz.html (2369 words)

	DNA Sequence Analysis (Site not responding. Last check: 2007-09-11)
		This will be where increased numbers of N's appear in the sequence, or where you can tell by looking at the dye peaks that the computer is beginning to have trouble with base calls or with skipping (or, alternatively, compressing) bases.
		Protein primary sequences are more stable, because mutations at the gene level that cause significant changes at the protein level may be detrimental to the organism.
		Protein sequence motifs are probably the most efficient generators of speculation when it comes to protein structure and function, which makes sequence motif searches well worth doing for any possibly structural sequence.
	www.cwu.edu /~verheys/seqanalysis.html (1418 words)

	EBI Tools: Blast, Fasta, Sequence Analysis, Homology Searches, Sequence Translation, Protein Annotation, Genomes, ...
		Structural Analysis - MSDfold or DALI can be used to query your protein structure and compare it to those in the Protein Data Bank (PDB).
		SRS3D is an integrated environment that allows the end-user to quickly and easily retrieve/visualise sequence structure and also feature data from primary, secondary and tertiary protein databases, is now publicly available from the EBI...
		Providing Web-based tools for microarray data analysis, Expression Profiler is a set of tools for clustering, analysis and visualization of gene expression and other genomic data.
	www.ebi.ac.uk /Tools/index.html (554 words)

	Sequence Analysis
		What are the underlying issues in the sequence (often glossed over and obscured in the overt action and in the dialogue, but possibly alluded to in the visuals)?
		Can the sequence be divided into individual segments (indicated, for instance, by shifts of location, jumps in time, intertitles, etc.)?
		" Are there intertitles, film-within-film sequences, obtrusive and self-conscious ("unrealistic") camera movements calling attention to the fact that the film is a construct?8.
	web.uvic.ca /german/439/seq.html (1334 words)

	Sequence analysis
		SAS is a tool which aims to bridge the gap between protein sequence and structural analysis, and to aid identification of a protein sequence, by using structural information to recognise distant homologues.
		Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
		sequence to a database of protein blocks, retrieve blocks, and create new blocks, respectively.
	www.biochem.ucl.ac.uk /bsm/BCSB/bioinfo_resources/seq_analysis.htm (458 words)

	HUBI : Nucleic acid sequence analysis
		COA (Correspondence Analysis) : COA is suited for studying differenciation among codons or for examining trends in amino-acids composition.
		ORF Finder : graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database.
		FSED (FrameShift Error Detection) : is suited to the analysis of newly determinated sequences before their submission to the databases, the potential frameshift errors being readily resolved by examination of raw data such as gel readings.
	www.biocenter.helsinki.fi /bi/rnd/biocomp/prog2.html (1057 words)

	Affymetrix - GeneChip-compatible™ Software Solutions Catalog - DNA Sequence Analysis
		This set of applications provides DNA sequence analysis tool for data coming from Affymetrix DNA Resequencing arrays or provides greater information about sequences represented on any class of Affymetrix microarrays.
		Built-in results analysis capabilities allow selection, sorting, and filtering of huge data sets of alignments and annotations based on species, gene names, protein families, and other scientific understanding linked to sequences and their annotations.
		Promoter sequences of regulated transcripts identified by ChipInspector can be extracted for further analysis.
	www.affymetrix.com /products/software/compatible/dna_sequence.affx (648 words)

	Sequence Analysis and DNA Plasmid
		Sequence analysis is exploring nucleotide or amino acid sequences, employing in silico (bioinformatics) techniques.
		Genchek is a genomics sequence analysis software package that facilitates analysis of all your genetic data, including complete genome, and SNPs (Single Nucleotide Polymorphism).
		For pricing and further information on sequence analysis tools click here,email or call 1(866)202-2100.
	www.ubi.ca /sequence-analysis.htm (336 words)

	How do we Sequence DNA? (via CobWeb/3.1 vn1.cs.wustl.edu) (Site not responding. Last check: 2007-09-11)
		After we sequence the fragments, we try to deduce from them the sequence of the original BAC DNA.
		At the bottom is the smallest fragment that's been terminated by ddC; that's probably the C closest to the end of the primer (which is omitted from the sequence shown).
		This is a plot of the colors detected in one 'lane' of a gel (one sample), scanned from smallest fragments to largest.
	seqcore.brcf.med.umich.edu.cob-web.org:8888 /doc/educ/dnapr/sequencing.html (1776 words)

	Bioinformatics - Wikipedia, the free encyclopedia (via CobWeb/3.1 vn1.cs.wustl.edu) (Site not responding. Last check: 2007-09-11)
		Another aspect of bioinformatics in sequence analysis is the automatic search for genes and regulatory sequences within a genome.
		For example, promoter analysis involves the elucidation and study of sequence motifs in the genomic region surrounding the coding region of a gene.
		The core of comparative genome analysis is the establishment of the correspondence between genes (orthology analysis) or other genomic features in different organisms.
	en.wikipedia.org.cob-web.org:8888 /wiki/Bioinformatics (2822 words)

	Sequence Analysis Tools
		Amphi Program - This program provides algorithms to calculate three amphipathic characteristics of a given amino acid sequence: (i) the hydrophobicity of segments of 7 amino acid residues,(ii) the hydrophobicity of segments of 19 amino acid residues, (iii) the amphipathy of alpha-helices of 20 residues, and (iv) the amphipathy of beta-strands of 10 residues.
		NIH BioInformatics and Molecular Analysis Section - Numerous computational tools and resources to unite advances in biology with those in computers, informatics, and networking for the genomic and genetic analysis fields of BioInformatics; division of the Computational Bioscience and Engineering Lab at the Center for Information Technology.
		SigmaScan Pro-Powerful Image Analysis for Your PC - SigmaScan Pro 5.0 provides a complete image analysis package for studying the structure and size of objects in your visual information.
	www.mcdb.ucla.edu /Research/Lin/links/sequence_analysis (1148 words)

	EBI Tools: Sequence Analysis. Sequence Translation, Validation, Alignments, Gene Prediction
		Sequence analysis encompasses the use of various bioinformatic methods to determine the biological function and/or structure of genes and the proteins they code for.
		ClustalW is use to align DNA or protein sequences in order to elucidate their relatedness as well as their evolutionary origin.
		Compare a protein sequence or a protein profile HMM to a DNA sequence.
	www.ebi.ac.uk /Tools/sequence.html (367 words)

	SWBIC - DNA Sequence Analysis (Site not responding. Last check: 2007-09-11)
		User may enter sequence or datafile to be searched, and sequence of pattern searched for.
		Its goal is "to facilitate large-scale semi-automatic sequence analysis projects, leveraging human intelligence by simplifying laborious tasks, without taking human judgment out of the loop."
		The Sequence Manipulation Suite is a collection of web-based programs for analyzing and formatting DNA and protein sequences.
	www.swbic.org /links/1.4.3.php (1070 words)

	Softgenetics - Software Power Tools for Genetic Analysis
		Mutation Analysis Software from sequence traces…Mutation Surveyor™ and Mutation Explorer® utilize our patent pending physical trace comparison technology providing accuracy >99% when using bi-directional Phred 20 quality sequence traces.
		The software is an excellent tool for both discovery and diagnostic applications, and accepts sequence traces from all major sequencing systems such as those marketed by Applied BioSystems, Foster City CA, or Amersham Megabace systems, and is compatible with either terminator or primer chemistries.
		GeneMarker is equally useful in performing Microsatellite analysis, Multiplex Ligation-dependent Probe Amplification (MLPA) Amplified Fragment Length Polymorphism (AFLP and fAFLP) analysis, Terminal-Restiction Fragment Length Polymorphism (T-RFLP) microbial fingerprinting, Quantitative Analysis of DNA fragments, STR Analysis, SnapShot®, SNPlex®, or LOH analysis.
	www.softgenetics.com (425 words)

	ProSAL - Protein Sequence Analysis Launcher
		You will then be presented with a page with ready-made forms to submit to a variety of Web-based protein sequence analysis facilities.
		The way this server works, is that a little Perl CGI script reads your sequence and pastes it into a template form.
		Your sequence is never stored on disk here, nor does anyone receive a copy of it.
	xray.bmc.uu.se /sbnet/prosal.html (465 words)

	Sequence Analysis Tools (Site not responding. Last check: 2007-09-11)
		Protein Translator for determining the protein sequence encoded by a DNA or RNA sequence.
		Sequence Pattern Finder for locating sequences matching a particular pattern in a given DNA sequence.
		Sequence Massager for formatting and otherwise manipulating nucleic acid sequences.
	www.attotron.com /cybertory/analysis.htm (139 words)

	Sequence Analysis
		Choose one of the following links to reach the major servers for sequence analysis, or choose a more specific link from the menu below.
		The Baylor College of Medicine Search Launcher is an on-going project to organize molecular biology-related search and analysis services available on the WWW by function by providing a single point-of-entry for related searches (e.g., a single page for launching protein sequence searches using standard parameters).
		This server is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE.
	www.biu.ac.il /LS/Services/units/bio/seqanal.html (397 words)

	Fundamentals of Sequence Analysis, 1998-1999
		The vast amount of sequence and sequence related information which the many genome projects have been accumulating has led several sites to develop and distribute viewers.
		Those sequences are then clustered by similarity with each other and with the known genes.
		Frequently a similar protein is discovered in humans, in which case a visit to the OMIM database may prove useful, especially concerning the range of possible phenotypes for mutant forms of this gene.
	seqaxp.bio.caltech.edu /www/seqanalysis/lecture_10.html (1738 words)

	ExPASy - Tools (via CobWeb/3.1 vn1.cs.wustl.edu) (Site not responding. Last check: 2007-09-11)
		Experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified Swiss-Prot entry or from a user-entered sequence, and mass differences are used to better characterize the protein of interest.
		SearchXLinks - Analysis of mass spectra of modified, cross-linked, and digested proteins whose amino acid sequence is known, from Caesar, Germany
		LOOPP - Sequence to sequence, sequence to structure, and structure to structure alignment
	www.expasy.org.cob-web.org:8888 /tools (2175 words)

	Forsburg Lab: Sequence analysis Sites
		Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein families.
		Regulatory Sequence Analysis Tools (RSAT) website provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences.
		Meta analysis of coexpression data from the Kim lab.
	www-rcf.usc.edu /~forsburg/seqlinks.html (768 words)

	DNA sequence analysis
		repeats : scans a dna sequence, looking for tandemly repeated patterns where the period of the repeat has a user specified size from 1 to 32 nucleotides (G. Benson).
		satellites: identifying satellites and periodic repetitions in a sequence (MF.
		It was designed to simplify Multivariate Analysis (MVA) of codon usage (John Peden).
	bioweb.pasteur.fr /seqanal/dna/intro-uk.html (329 words)

	Biological Information Resource v2.5, University of Washington
		Four bioinformatics workstations have been established in the Health Sciences Library and in the Department of Pathobiology for software development and bioinformatics training.
		Sequence analysis software is currently being developed for use through a Web browser.
		PABIO 536 "Bioinformatics and Gene Sequence Analysis" (Instructor -
	courses.washington.edu /bioinfo/BIR (341 words)

	ONLINE ANALYSIS TOOLS
		Analysis of nucleotide and protein sequence data was initially restricted to those with access to complicated mainframe or expensive desktop computer programs (for example PC/GENE, Lasergene, MacVector, Accelrys etc.).
		The availability of online tools permits even the novice molecular biologist the opportunity to derive a considerable amount of useful nformation from nucleotide or protein sequence data.
		For those with no experience I have provided three sequences: (a) a DNA sequence, (b) a protein sequence, and (c) four protein sequences presented in FASTA format.
	molbiol-tools.ca (258 words)

	BCM Search Launcher: Sequence Utilities
		All sequences must be in the same format type (e.g., Fasta format)
		RepeatMasker-identify and mask repeats in DNA sequences (UW) [
		Sequence Chopover - cut a large protein/DNA sequence into smaller ones with certain amounts of overlap (BCM).
	searchlauncher.bcm.tmc.edu /seq-util/seq-util.html (143 words)

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