Sequence (biology)

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Topic: Sequence (biology)

Note: these results are not from the primary (high quality) database.

In the News (Thu 24 Dec 09)

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	Catalogue of Molecular Biology Programs
		AC BC00485 NAME PromFind DOMAIN Sequence analysis DESCRIPTION PromFind is a DOS-based computer program that accepts a DESCRIPTION DNA sequence as input in one of several formats, and produces DESCRIPTION as output the same sequence in GenBank or EMBL format with DESCRIPTION a feature table added to annotate the location of putative DESCRIPTION promoter regions.
		RA Gibson T.J., Rice P.M., Thompson J.D., Heringa J.; RT "KH domains within the FMR1 sequence suggest that RT fragile X syndrome stems from a defect in RNA metabolism."; RL Trends Biochem.
		AC BC00566 NAME CloneIt DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Restriction maps DESCRIPTION Molecular biologists often have to sub-clone DESCRIPTION plasmidic vectors: a DNA plasmid is cleaved and ligated DESCRIPTION with an exogen DNA fragment previously excised from an DESCRIPTION other plasmid.
	corba.ebi.ac.uk /Biocatalog/Sequence_analysis.html

	Computational Molecular Biology
		This will include a brief review of basic molecular biology (structure & evolution of genes, genomes and proteins), probabilistic models of sequences and of sequence evolution, computational gene identification, pairwise sequence comparison and alignment (algorithms and statistical issues), multiple sequence alignment and evolutionary tree construction, and protein sequence/structure relationships.
		2 quarters of molecular biology, biochemistry, and/or genetics (the equivalent of GENOME 371/372, and/or BIOC 440/441)
		A 2-quarter course on protein and DNA sequence analysis and molecular evolution.
	depts.washington.edu /cmolbiol (1462 words)

	Biocompare News - Chicken Genome Assembled
		In addition, using the Gallus gallus genome sequence assembled by Washington University as a reference framework, an international team, led by the Beijing Genomics Institute in China and supported by the Wellcome Trust in Britain, has created a map of genetic variation for three different strains of domestic chickens.
		The Washington University researchers have deposited the initial assembly, which is based on seven-fold sequence coverage of the chicken genome, into the public database, GenBank (www.ncbi.nih.gov/Genbank).
		To facilitate comparative genomic analysis, the researchers also have aligned the draft version of the chicken sequence with the human sequence.
	news.biocompare.com /newsstory.asp?id=29121 (1462 words)

	Indiana University Department of Biochemistry & Molecular Biology
		One of the central, unsolved problems in molecular biology is the code by which a given amino acid sequence determines a 3D fold.
		The Central Dogma of molecular biology is that DNA sequence determines messenger RNA sequence, which in turn determines amino acid sequence.
		This trail has led to a new classification scheme for molecular recognition, a new classification scheme for structure/sequence relationships, and a proposed critical role for disordered regions in the evolution of molecular biological networks.
	www.biochemistry.iupui.edu /personnel/Dunker (587 words)

	Indiana University Department of Biochemistry & Molecular Biology
		One of the central, unsolved problems in molecular biology is the code by which a given amino acid sequence determines a 3D fold.
		The Central Dogma of molecular biology is that DNA sequence determines messenger RNA sequence, which in turn determines amino acid sequence.
		This trail has led to a new classification scheme for molecular recognition, a new classification scheme for structure/sequence relationships, and a proposed critical role for disordered regions in the evolution of molecular biological networks.
	www.biochemistry.iupui.edu /personnel/Dunker (587 words)

	Dr. Patrick K. Bender
		sequence-array chip technology), the Molecular Biology Laboratory is initiating new efforts in the application of sequence-arrays to the study of cell aging.
		The area of his studies was cell biology under the mentorship of Dr. Lionel I. Rebhun.
		In addition, this laboratory anticipates increased efforts in the Primate Resource Initiative with emphasis on the development of primate sequence-array chips for the classification of African primates based on mitochondrial sequences.
	coriell.umdnj.edu /science/bender.html (745 words)

	Computational Biology or Bioinformatics references
		The University of California, Santa Cruz, bioinformatics (computational biology) research group models the primary (sequence) and secondary structures of DNA, RNA, and protein sequences, using hidden Markov Models (SAM=Sequence Alignment and Modeling System) and stochastic context-free grammars.
		This site provides some useful information including pointers to several molecular biology database (for nucleic acids, proteins, enzymes, and others), documentation related to sequence of analysis, journal references and links to other bilogy related sites.
		The SUPERFAMILY database uses the SAM-T99 technology with seeds from the SCOP domain library, to provide reasonable sequence-based domain identification.
	www.cse.ucsc.edu /~karplus/compbio_pages.html (745 words)

	Computational Molecular Biology
		This will include a brief review of basic molecular biology (structure & evolution of genes, genomes and proteins), probabilistic models of sequences and of sequence evolution, computational gene identification, pairwise sequence comparison and alignment (algorithms and statistical issues), multiple sequence alignment and evolutionary tree construction, and protein sequence/structure relationships.
		Students from diverse undergraduate majors, including biology, chemistry, computer science, mathematics, physics, statistics, and related areas, are encouraged to apply.
		The CMB program is just one of several at the University of Washington which focus on the use of computational, statistical or mathematical methods to study problems in biology.
	depts.washington.edu /cmolbiol (1462 words)

	Computational Molecular Biology
		This will include a brief review of basic molecular biology (structure & evolution of genes, genomes and proteins), probabilistic models of sequences and of sequence evolution, computational gene identification, pairwise sequence comparison and alignment (algorithms and statistical issues), multiple sequence alignment and evolutionary tree construction, and protein sequence/structure relationships.
		These are the central computational methods required to determine the "periodic table of biology", i.e.
		The CMB program is just one of several at the University of Washington which focus on the use of computational, statistical or mathematical methods to study problems in biology.
	depts.washington.edu /cmolbiol (1462 words)

	Life Sequence
		#5: Computational Biology and Chemistry - Publishes original papers and reviews in all areas of computational life sciences, such as nucleic acid and protein sequence research, molecular evolution, molecular genetics (functional genomics and proteomics), theory and practice of either biology-specific or chemical-biology-specific modeling, and structural biology of nucleic acids and proteins.
		Life Sequence (2003) is an album by the American ambient musician Steve Roach.
		#7: Ti Kai Moy's Original MIDI Compositions - Midi Sequences of original pop and alternative music compositions, music with Eastern influence songs and lyrics about love, the struggles and pains in life, social and political issues.
	omniknow.com /essays/Life_Sequence.html (1462 words)

	Glossary of Biochemistry and Molecular Biology
		Molecular biology: The biochemical study of the genetic basis for phenotype.
		In molecular biology, it has acquired the more specific verbal usage for the transfer onto DNA of a radiolabeled phosphate group.
		Base: In molecular biology, this term refers to the purine bases adenine and guanine, and the pyrimidine bases uracil, thymine, and cytosine, or modification of these bases.
	www.geocities.com /rgklink/glossary/molglos.html (1462 words)

	Examples
		Instead of doing a sequence to structure alignment with only the input sequence against the list of known structures, the program will first find sequences of high sequence homology to the input sequence and align those to the list of known structures as well.
		General topics to be explored include the history of computer games, character development, the game development process, and violence in media and video games.
		General topics to be explored include character development, the history of computer games, and violence in media and video games.
	www.cs.cornell.edu /degreeprogs/ugrad/CSMajor/CoursesandResearch/RegisteringforCS490/Examples/index.htm (1462 words)

	Transcription and Translation
		The term translation comes from the idea that the process involves the changing of sequence information from the language of nucleic acids (i.e., codon-based) to the language of polypeptides (i.e., amino acid based).
		This universality of codon usage, combined with the apparent arbitrary correspondence of codon sequence to amino acid, is extremely strong evidence for the existence of a common ancestor to all extant organisms.
		Though two or more reading frames may overlap, their products won't share amino acid sequences because various overlapping reading frames are not in frame (that is, each would be considered a unique gene loci, though clearly nucleotide sequences of such overlapping genes would be constrained evolutionarily by the sequences of the genes they overlap).
	www.mansfield.ohio-state.edu /~sabedon/biol1065.htm (1462 words)

	biosoft-free.text
		Author: Heikki Lehva, lehvaslaiho@cc.helsinki.fi Archive:: iubio/mac/cgr, ebi/mac/cgr Clustal W M, W, O A multiple sequence alignment program, which is widely used and described in the article Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
		Author: Ned Mantei Archive: iubio/mac/analyze-signalase* Ancestor W Ancestor is designed to infer ancestral amino acid sequences from a set of homologous amino acid sequences whose phylogenetic relationships are known.
		Author: Ilya N. Shindyalov, Philip E. Bourne, bourne@sdsc.edu Home: ftp://ftp.sdsc.edu/pub/sdsc/biology/WPDB/ Yeast Strain M This is a Hypercard stack for cataloguing the genotypes of S. cerevisiae yeast strains.
	iubio.bio.indiana.edu:7131 /soft/molbio/docs/biosoft-free.text (10114 words)

	A Molecular Biology Glossary
		Usually, protein translation can only start at a methionine codon (although this codon may be found elsewhere within the protein sequence as well).
		While not itself translated, this region may have sequences which alter the translation efficiency of the mRNA, or which affect the stability of the mRNA.
		Sometimes, however, people speak of "translating" the DNA or RNA when they are merely reading the nucleotide sequence and predicting from it the sequence of the encoded protein.
	seqcore.brcf.med.umich.edu /doc/educ/dnapr/mbglossary/mbgloss.html (10114 words)

	Mathematical Biology - National Institute for Medical Research
		In the division of Mathematical Biology, we develop methods of sequence analysis to aid in the identification of novel genes from the sequences of the human and other genomes.
		We are continually improving and expanding these methods through both fundamental research on algorithms and continual comparison and analysis of the sequences and structures that are known.
		Our methods work mainly with the protein sequence that is derived directly from the gene sequence.
	mathbio.nimr.mrc.ac.uk (168 words)

	templatemain
		The predicted primary structures from the PELE program within the Biology Workbench turned out to be only a portion of the primary sequence imported from NCBI database.
		The only one of the species that did not have a protein structure predicted in NCBI or the Biology Workbench was the click-beetle (P. termit); he is omitted from these phylogenetic analyses.
		The structures that I predicted, both primary and secondary are much shorter in length than the known structures from NCBI because the sequence that I used in the Workbench was a shorter sequence.
	www.wou.edu /las/natsci_math/biology/boomer/Bio301/Compprojects/Shipley/webtemplate/templatemain.html (168 words)

	UNSW Embryology- Chicken Development
		Fertilized eggs can be easily maintained in humidified incubators and during early stages of development the embryo floats on to of the egg yolk that it is using for nutrition.
		Quicktime movie sequence 4 (1.5 MB) Sequence showing transplantation and grafting of donor quail neural tube and neural crest into the chick host; at the end of this sequence, you see the host chick embryo 5 hours later with its healed in graft.
		The chicken (taxon- Gallus gallus) embryo develops and hatches in 20-21 days and has been extensively used in embryology studies.
	embryology.med.unsw.edu.au /OtherEmb/Chicken.htm (168 words)

	Computational Biology Branch
		The expertise of the group is concentrated in sequence analysis, protein structure/function analysis, and gene identification, yet research interests cover a wide range of topics in computational biology and information science.
		Members also provide leadership and guidance to the extramural community by planning and organizing scientific consortia to determine the most effective use of public sequence resources for large-scale or high-throughput experimental biology.
		The research program in the Computational Biology Branch is carried out by nine Senior Investigators and a number of Staff Scientists and Postdoctoral Fellows and focuses on theoretical, analytical and applied approaches to a broad range of fundamental problems in molecular biology.
	www.ncbi.nlm.nih.gov /CBBresearch (295 words)

	Computational Biology or Bioinformatics references
		The University of California, Santa Cruz, bioinformatics (computational biology) research group models the primary (sequence) and secondary structures of DNA, RNA, and protein sequences, using hidden Markov Models (SAM=Sequence Alignment and Modeling System) and stochastic context-free grammars.
		This site provides some useful information including pointers to several molecular biology database (for nucleic acids, proteins, enzymes, and others), documentation related to sequence of analysis, journal references and links to other bilogy related sites.
		Pointers to conferences run by the International Society for Computational Biology (includes ISMB and PSB).
	www.cse.ucsc.edu /~karplus/compbio_pages.html (3374 words)

	Mathematical Biology - National Institute for Medical Research
		In the division of Mathematical Biology, we develop methods of sequence analysis to aid in the identification of novel genes from the sequences of the human and other genomes.
		We are continually improving and expanding these methods through both fundamental research on algorithms and continual comparison and analysis of the sequences and structures that are known.
		Our methods work mainly with the protein sequence that is derived directly from the gene sequence.
	mathbio.nimr.mrc.ac.uk (3374 words)

	Open Directory - Science: Biology: Bioinformatics: Software
		Molecular Evolutionary Genetics Analysis (MEGA2) software - Provides free downloadable MEGA2 software for use in comparative sequence analysis of genetic data.
		It includes a sequence editor, several sequence aligners, phylogeny reconstruction tools, probe/primer search and generation, genome annotation and visualization.
		An open source project started by the EMBnet community in order to replace proprieatry systems like GCG.
	dmoz.org /Science/Biology/Bioinformatics/Software (3374 words)

	DNA - Psychology Central
		Watson and Crick proposed the central dogma of molecular biology in 1957, describing the process whereby proteins are produced from nucleic DNA.
		As a simple example, research on string searching algorithms, which find an occurrence of a sequence of letters inside a larger sequence of letters, was motivated by DNA research, where it is used to find specific sequences of nucleotides in a large sequence.
		A number of other problems, including simulation of various abstract machines, the boolean satisfiability problem, and the bounded version of the Post correspondence problem, have since been analyzed using DNA computing.
	psychcentral.com /psypsych/DNA (5855 words)

	Loyola Univ. Health Univ. Health Sys- Microbiology & Immunology: Web-Walker 2100 Molecular Biology & Biomedical Information
		BCM Search Launcher: This site organizes molecular biology-related search and analysis services available on the WWW by function, and to provide a single point-of-entry for related searches (e.g., a single page for launching protein sequence searches using standard parameters, also nucleic acid sequence searches and multiple sequence alignments).
		European Molecular Biology Laboratory (EMBL): The aim of this server is to provide an online information service of activities at EMBL.
		EMBL Predict Protein: European Molecular Biology Laboratory email service for prediction of protein structure (secondary structure, solvent accessibility, transmembrane helices, multiple alignments).
	www.meddean.luc.edu /lumen/DeptWebs/microbio/web-walk/mol.htm (874 words)

	Catalogue of Molecular Biology Programs
		RA XU Y., Einstein J.R., Mural R.J., Shah M.B., Uberbacher E.C.; RT "An Improved System for Exon Recognition and Gene Modeling RT in Human DNA Sequences."; RL Proceedings of The 2nd International Conference on Intelligent RL Systems for Molecular Biology, AAAI Press (August 1994).
		That means, it may serve DESCRIPTION lab-workers in molecular biology and genetic engineering to DESCRIPTION monitor the DNA-cloning process.
		AUTHOR Maria Jesus Martin, Joaquin Dopazo RA Martin M.J., Gonzalez-Candelas F., Sobrino F., Dopazo J.; RT "A method for determining the position and size of optimal RT sequence regions for phylogenetic analysis."; RL J. Mol.
	corba.ebi.ac.uk /Biocatalog/Sequence_analysis.html (874 words)

	The Central Dogma - Introduction
		The "central dogma" in biology holds that DNA sequence is transcribed into RNA sequence which is then translated into amino acid sequence (and, ultimately, to protein structure and function).
		Much of the information provided here can also be found in good molecular biology textbooks.
		This process, known as gene expression, can seem like an extremely complex process to those who are unfamiliar with it.
	www.unc.edu /cell/files/extensions/dogma/intro.html (874 words)

	Visualizing the Central Dogma of Molecular Genetics
		The central dogma of molecular biology states that information encoded in DNA is transcribed into RNA; RNA is subsequently translated into an amino acid sequence; and the amino acid sequence is modified and folded into a functional protein.
		The first tool is the Biology Workbench which is maintained by the San Diego Supercomputer Center and supported by US tax dollars.
		Begin your investigation by downloading a.pdf version of "Sickle Cell Anemia: Understanding the Molecular Biology." (Unless you already have a copy.) This guide provides step-by-step instructions for completing your investigation.
	www.physci.wsc.ma.edu /intscimath/02spring/centdogma.html (331 words)

	The Merck Distinguished Seminar Series in Computational Biology and Chemistry
		These results encouraged us to consider possible roles of unfolded protein states in the realm of molecular biology, thereby leading us to a new classification scheme for structure/sequence relationships, a new classification scheme for molecular recognition, and a proposed critical role for disordered regions in the evolution of molecular biological networks.
		The extended Central Dogma of molecular biology is simply represented as DNA --> RNA --> amino acid sequence --> 3D structure --> function, where the last three steps comprise the current protein structure/function paradigm.
		If verified, our predictions will ultimately require a significant restructuring of the extended Central Dogma of molecular biology in order to include the important functions carried out by intrinsically disordered proteins.
	www.cmu.edu /mcs/Merck/MerckSeminar02Abstract.html (331 words)

	PLU Biology Homepage
		Completion of this sequence (or an equivalent general biology sequence at another institution) is required before upper-division biology courses can be taken.
		To learn biology is more than to learn facts: it is to learn how to ask and answer questions, how to develop strategies which might be employed to obtain answers, and how to recognize and evaluate the answers which emerge.
		Students who plan to apply biology credits earned at other institutions toward a PLU degree with a biology major should be aware that at least 14 hours in biology, numbered 324 or higher and including 499, must be earned in residence at PLU.
	www.nsci.plu.edu /biol (753 words)

	Homology (biology) - Wikipedia, the free encyclopedia
		Homology has to be distinguished from analogy; for instance, the wings of insects, the wings of bats and the wings of birds are analogous but not homologous, this phenomenon is known as Homoplasy.
		Homology among proteins and DNA is often concluded on the basis of sequence similarity, especially in bioinformatics.
		In genetics, homology is used in reference to protein or DNA sequences, meaning that the given sequences share a common ancestor.
	en.wikipedia.org /wiki/Homology_(biology) (720 words)

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In the News (Thu 24 Dec 09)