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Topic: Consensus sequence

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	Consensus sequence
		Consensus sequence is a genetic sequence found with minor variations and similar functions in widely divergent organisms or genetic locations.
		In molecular biology and bioinformatics, one major goal is to parse genetic sequences and employ methods of statistical classification for the identification of consensus sequences.
		A consensus sequence can vary in length and can be have multiple instances in a single genome (the full set of chromosomes of an individual, or the total number of genes in such a set).
	www.iscid.org /encyclopedia/Consensus_sequence (290 words)

	Consensus sequence - Wikipedia, the free encyclopedia
		In molecular biology and bioinformatics, a consensus sequence is a way of representing the results of a multiple sequence alignment, where related sequences are compared to each other, and similar functional sequence motifs are found.
		This is a graphical representation of the consensus sequence, in which the size of a symbol is related to the frequency that a given nucleotide (or amino acid) occurs at a certain position.
		A consensus sequence may be a short sequence of nucleotides which is found several times in the genome and is thought to play the same role in its different locations.
	en.wikipedia.org /wiki/Consensus_sequence (464 words)

	CLC bio: Consensus sequence determination and management
		The consensus sequence is based on every single positions in the alignment and reflects an artificial sequence which resembles the sequence information of the alignment, but only as one single sequence.
		If all sequences of the alignment is 100% identical the consensus sequence will be identical to all sequences found in the alignment.
		The consensus sequence can be copied and pasted into a separate view for further analyses.
	www.clcbio.com /index.php?id=466 (160 words)

	Consensus sequence -- Facts, Info, and Encyclopedia article (Site not responding. Last check: 2007-10-28)
		Specific (additional info and facts about sequence motif) sequence motifs can function as (additional info and facts about regulatory sequence) regulatory sequences controling biosynthesis, or as (additional info and facts about signal sequence) signal sequences that direct a molecule to a specific site within the cell or regulate its maturation.
		Since the regulatory function of these sequences is important, they are thought to be conserved across long periods of ((biology) the sequence of events involved in the evolutionary development of a species or taxonomic group of organisms) evolution.
		Finally splice sites (sequences immediately surrounding the (Sequence of a gene's DNA that transcribes into protein structures) exon- (Sequence of a eukaryotic gene's DNA that is not translated into a protein) intron boundaries) can also be considered as consensus sequences.
	www.absoluteastronomy.com /encyclopedia/c/co/consensus_sequence.htm (458 words)

	Sequence motif - Wikipedia, the free encyclopedia
		A sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance.
		When a sequence motif appears in the exon of a gene, it may encode the "structural motif" of a protein; that is a stereotypical element of the overall structure of the protein.
		a sequence of elements of the pattern notation matches a sequence of amino acids if and only if the latter sequence can be partitioned into subsequences in such a way that each pattern element matches the corresponding subsequence in turn.
	en.wikipedia.org /wiki/DNA_motif (989 words)

	Electric Genetics - stackPACK v2.2
		The program assigns internal accession numbers to the clonelinks, clusters, contigs and consensus sequences produced in the clustering pipeline and these, as well as the original sequence accession numbers, may be used to query the viewer.
		Consensus accessions are internal numbers used to track multiple consensus sequences and may also be used to query the viewer.
		This contig Consensus View corresponds to the PHRAP Consensus Sequence, and is also displayed when clicking on the first icon from the left next to the contig accession number in the cluster tree.
	genomics.msu.edu /stackpack/support/probe.html (5383 words)

	Affymetrix - Probe Set Display Manual
		Alignments of the consensus, target and probe sequences against the golden path (the public draft of the assembled human genome sequence) are also displayed.
		Sequences are included in the alignment display only if 40% of the query sequence aligns to the subject or vice versa i.e., 40% of the subject aligns to the query.
		The subject sequence bars are shaded according to the percent identity with the query sequence.
	affymetrix.com /support/technical/manual/probe_set_display_manual.affx (1715 words)

	LineUp
		Sequences can be placed anywhere on the surface as long as two sequences in the same row do not collide.
		An optional consensus sequence can be generated as a function of the rest of the sequences in a sequence group, or, like any other sequence, typed in by you.
		The consensus sequence is unique in that, because it will likely extend to all columns determined by the other sequences, no other sequence may share its row.
	www.biology.wustl.edu /gcg/lineup.html (5942 words)

	R: Sequence Consensus for an Alignment
		Determines the consensus sequence for a given alignment at a given identity cutoff value.
		a numeric value beteen 0 and 1, indicating the minimum sequence identity threshold for determining a consensus amino acid.
		A vector containing the consensus sequence, where ‘-’ represents positions with no consensus (i.e.
	mccammon.ucsd.edu /~bgrant/bio3d/html/consensus.html (55 words)

	ALIGN_CONSENSUS -- consensus sequence alignment (Site not responding. Last check: 2007-10-28)
		This command is similar to ALIGN except that a consensus alignment of two blocks of sequences is produced.
		A consensus alignment is obtained from a consensus similarity matrix using the specified gap penalties and the global dynamic programming method.
		The consensus similarity matrix is obtained by aligning the two blocks of sequences many times with different parameters and methods and counting how many times each pair was aligned.
	bob.usuf2.usuhs.mil /bid510/modeller_manual/node99.html (217 words)

	EGCG plotalign (Site not responding. Last check: 2007-10-28)
		The consensus is found by finding the symbol in the column for which its comparison to all of the symbols in the column (including itself) yields the greatest number of votes.
		The consensus is the symbol that had the largest number of votes (vote weights) in the column.
		If several of your sequences are very similar, you may not want their votes to dominate the consensus for the column.
	cmgm.stanford.edu /EGCGdoc/source/plotalign.html (1526 words)

	The Consensus Sequence Hall of Fame
		Sequence logos are not consensus sequences, although it is possible to read the consensus from them.
		holoenzyme, a general rule is that mutations that decrese a promoters's agreement with the consensus decrease the frequency of transcription initiation, and mutations that increase consensus agreement increase initiation frequency (20).
		Fur forms a dimer together with ferrous iron and binds to a consensus sequence (Fur-box) that overlaps the promoters of iron regulated genes, resulting in the inhibition of transcription.
	www-lmmb.ncifcrf.gov /~toms/consensus.html (1247 words)

	ASAP-Glossary (Site not responding. Last check: 2007-10-28)
		The consensus is later used to probe contigs to find the genomic sequence.
		Length of the EST/mRNA sequence aligned to the genomic sequence.
		The genomic sequence corresponding to a particular UniGene cluster.
	www.bioinformatics.ucla.edu /HASDB/doc/glossary.html (1214 words)

	[No title]
		Any sequence data that could not be assembled in the contig sequence will still be present as a sequence icon in the project window.
		The lowest sequence is the consensus sequence generated from the alignment.
		Sequencher allows you to trim ends based on either the frequency of ambiguous base calls at the ends of the sequence, or it the Phred data is available, by the frequency of low confidence base calls.
	www.msu.edu /~rbritton/mmg433/labs/Lab3-2005.doc (1050 words)

	CCDS Report for Consensus CDS (Site not responding. Last check: 2007-10-28)
		The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality.
		These two new icons are in the Links column for each sequence ID shown in the table of sequence IDs for a CCDS.
		The human and mouse genome sequence is now sufficiently stable to start identifying those gene placements that are identical, and to make those data public and supported as a core set by the three major public genome browsers.
	www.ncbi.nlm.nih.gov /projects/CCDS (1190 words)

	The Consensus Sequence Hall of Fame
		The logo serves the function of describing the overall picture of many binding sites, but unlike a consensus sequence it is highly sensitive to variation in the sequence conservation.
		Sequence logos are not consensus sequences, although it is possible to read the consensus from them.
		Fur forms a dimer together with ferrous iron and binds to a consensus sequence (Fur-box) that overlaps the promoters of iron regulated genes, resulting in the inhibition of transcription.
	www.ccrnp.ncifcrf.gov /~toms/consensus.html (1286 words)

	Drug Discovery & Development (Site not responding. Last check: 2007-10-28)
		One of the set of proteins with related sequences (isoforms) that may be generated by alternate splicing of exons within a single mRNA.
		Anions migrate to the anode of an electrophoretic gel.
		Three-nucleotide sequence of a transfer RNA (tRNA) that is complementary to the three-nucleotide codon of an mRNA.
	dddmag.com /scripts/Glossary.asp?...&SEARCHWORD=Consensus+sequence (2450 words)

	EMBOSS: cons
		To obtain the consensus, the sequence weights and a scoring matrix are used to calculate a score at each position in the alignment.
		Where no consensus is found at a position i, an 'n' or an 'x' character is output; (depending on it being a DNA or protein sequence).
		Therefore, if this is set to the number of sequences in the alignment only columns of identities contribute to the consensus.
	www.sacs.ucsf.edu /Documentation/emboss/cons.html (839 words)

	HIV Sequence Database: SeqPublish Submission Form
		The first sequence in the input alignment will be selected as the reference sequence for the entire analysis.
		The fraction of characters in a column of the alignment needed to establish unanimity (shown as a capital letter) for that column.
		The ends of short sequences are padded with trailing blanks to make them the same length as longer sequences.
	www.hiv.lanl.gov /content/hiv-db/SeqPublish/seqpublish.html (330 words)

	Determination of the consensus binding sequence for the purified embryonic heat shock factor 2 -- Manuel et al. 269 ... (Site not responding. Last check: 2007-10-28)
		Determination of the consensus binding sequence for the purified embryonic heat shock factor 2 -- Manuel et al.
		Determination of the consensus binding sequence for the purified embryonic heat shock factor 2
		The consensus binding sequence for the purified embryonic mHSF2 was obtained from the sequences of individual Sel6 clones.
	content.febsjournal.org /cgi/content/full/269/10/2527 (6187 words)

	SH3 domain
		It is used in signal transduction proteins, often in pathways involving tyrosine kinases.
		The sequence binds to the hydrophobic pocket of the SH3 domain.
		SH3 domains are often found in functions concerning the cytoskeleton, the ras protein, and the src kinase.
	www.brainyencyclopedia.com /encyclopedia/s/sh/sh3_domain.html (142 words)

	A Glossary for Molecular Information Theory and the Delila System
		The simplest form of a consensus sequence is created by picking the most frequent base at some position in a set of aligned DNA, RNA or protein sequences such as binding sites.
		Rogan and Schneider (1995) a case is shown where a patient was misdiagnosed because a consensus sequence was used to interpret a sequence change in a splice junction.
		Note that sequence logos are an average picture of a set of binding sites (which is why logos can have several letters in each stack) while sequence walkers are the individuals that make up that average (which is why walkers have only one letter per position).
	www.ccrnp.ncifcrf.gov /~toms/glossary.html (10999 words)

	WebLogo - About
		Sequence logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment developed by Tom Schneider and Mike Stephens.
		The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position.
		The Look and Feel of the sequence logo generation form was inspired by the GIF/PNG-Creator for 2D Plots of Chemical Structures.
	weblogo.berkeley.edu (279 words)

	EGCG fragment_assembly
		The contig percentage figures are calculated relative to the length of the consensus sequence.
		Where the consensus sequence does not agree with every fragment in the contig, the consensus sequence is highlighted.
		Base positions in the consensus which agree with every fragment are not shown; other positions are highlighted by printing the base on the consensus line.
	biosci.cbs.umn.edu /software/egcg/fragment_assembly.html (3117 words)

	[No title]
		A set of DNA -> Find the consensus sequence by finding the most occurrences -> deselect the consensus sequence and make selective sequence -> do branch and bound method -> return the final result This design is designed for large input DNA sequence and larger set of DNA sequence will see the larger difference.
		AAGGCCT Error Analysis to Consensus Sequence: The maximum of errors for all sequences is generated.
		Only letters that appear in the column for that index will be used to generate this series of sequences, notice that each column uses only two letters, since the other letters were not used in the original column of the input sequences.
	www2.hawaii.edu /~thuong/Biol.doc (1647 words)

	SAM: UCSC's Sequence Alignment and Modeling System
		A linear hidden Markov model is a sequence of nodes, each corresponding to a column in a multiple alignment.
		Using a match state indicates that the sequence has a character in that column, while using a delete state indicates that the sequence does not.
		standard methods of sequence search is their ability to characterize an entire family of sequences.
	www.soe.ucsc.edu /research/compbio/sam.html (1181 words)

	Kozak consensus sequence in expression vector - BioForum
		As I understand the Kozak sequence is few bp upstream of ATG and a single G after ATG (gccgccaccATGg).
		The Kozak consensus sequence was originally defined as ACCAUGG following an analysis of the effects of single mutations surrounding the initiation codon (AUG) on translation of the preproinsulin gene by Kozak.
		So it is just a CONSENSUS sequence that greatly facilitate the initial binding of mRNA to the small subunit of the ribosome.
	www.protocol-online.org /forums/index.php?showtopic=2595 (245 words)

	STACK: Sequence Tag Alignment and Consensus Knowledgebase -- Christoffels et al. 29 (1): 234 -- Nucleic Acids Research
		Tissue-level consensus sequences are decomposed to their constituent
		The blue box indicates the region capturing the fibulin-1B isoform whereas sequences capturing fibulin-1C are surrounded by a red box.
		10 Wilcox,A.S., Khan,A.S., Hopkins,J.A. and Sikela,J.M. (1991) Use of 3' untranslated sequences of human cDNAs for rapid chromosome assignment and conversion of STSs: implications for an expression map of the genome.
	nar.oxfordjournals.org /cgi/content/full/29/1/234 (2365 words)

	How many clones need to be sequenced from a single forensic or ancient DNA sample in order to determine a reliable ...
		To use, cut and paste pre-aligned sequence data with a five character sequence identifier from a text file or Word document and click OK to run the calculation (based on Equations 4 and 5).
		The results (a consensus sequence, confidence levels for each nucleotide and a whole sequence confidence level) can be copied back into a text file or Word document if required.
		Figure 3 We input published clone sequences for the HVII region of the Neanderthal type specimen [Figure 1 (24)] into the Consensus Confidence program [clones B18.1–B18.13 and D20.1–D20.7; a total of 20 clone sequences, covering nucleotide positions 00124–00201, numbering after Anderson et al.
	nar.oxfordjournals.org /cgi/content/full/33/8/2549 (4382 words)

	[Biojava-l] Reading consensus sequence from phred/phrap ace files (Site not responding. Last check: 2007-10-28)
		In fact if I am not mistaken, there really is no such thing as a consensus sequence in an.ace file.
		The file consists of a list of contig sequences, the individual reads, and a bunch more data.
		In a finished assembly project the "consensus sequence" is just the longest contig.
	www.biojava.org /pipermail/biojava-l/2001-June/001280.html (405 words)

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