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Topic: Sequence alignment

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	Sequence alignment - Wikipedia, the free encyclopedia
		It is usually used to study the evolution of the sequences from a common ancestor, especially biological sequences such as protein sequences or DNA sequences.
		Sequence alignment can also be used to study things like the evolution of languages and the similarity between texts.
		This is an extension of Smith-Waterman, for pairwise alignment between a protein sequence and a nucleotide sequence.
	en.wikipedia.org /wiki/Sequence_alignment (1530 words)

	Biomedical Initiative - (Site not responding. Last check: 2007-11-07)
		Multiple sequence alignment is the process of aligning several related sequences, showing the conserved and unconserved residues across all of the sequences simultaneously.
		Global multiple sequence alignments are sequence alignments that require the participation of all sequence residues.
		A multiple sequence alignment shows the residue juxtaposition across the entire set of sequences; thus showing the conserved and unconserved residues across all of the sequences simultaneously.
	www.psc.edu /biomed/training/tutorials/sequence/msa (1428 words)

	Bioinformatics - Wikipedia, the free encyclopedia
		Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, and the modeling of evolution.
		A representative problem in bioinformatics is the assembly of high-quality DNA sequences from fragmentary "shotgun" DNA sequencing, while in computational biology, a representative problem might be statistical testing of a hypothesis of common gene regulation using data from mRNA microarrays or mass spectrometry.
		A variant of this sequence alignment is used in the sequencing process itself.
	en.wikipedia.org /wiki/Bioinformatics (2785 words)

	Sequence Alignment
		A sequence alignment is a scheme of writing one sequence on top of another where the residues in one position are deemed to have a common evolutionary origin.
		The idea of assigning a score to an alignment and then minimizing over all alignments is at the heart of all biological sequence alignment.
		A further breakthrough in alignment algorithms development was an algorithm that could compute an optimal alignment using computer memory only proportional to the length of one sequence instead of their product.
	lectures.molgen.mpg.de /Pairwise/SeqAli (767 words)

	Introduction to Sequence Alignment (Site not responding. Last check: 2007-11-07)
		Summary: This module is an introduction to pairwise sequence alignments between a query sequence and a sequence database, using NCBI's BLAST, and between a query sequence and a genome, using UCSC's BLAT.
		The score of each alignment is divided into one of 5 ranges by the five different colors in the color key provided, and the alignments are placed in the order of best scores first.
		Notice that the query cDNA sequence is missing a large region of DNA that is present in the chromosome.
	cnx.org /content/m11026/latest (2062 words)

	Information-Theoretic Sequence Alignment
		The information content of an alignment is split into two parts, that due to the differences between the two sequences and that due to the characters of the sequences.
		An alignment of two (or more) sequences is here treated as a hypothesis; it is just a possible way in which characters of one sequence may be matched with characters of another sequence.
		The alignment method that is being described is not limited to this case and the use of `repeated-runs' is not meant to imply that it is a good model of DNA, say.
	www.csse.monash.edu.au /~lloyd/tildeStrings/Compress/1998TR98-14-align.html (3341 words)

	[No title]
		Note that if you are comparing a sequence of length N with another sequence of length M, then the total number of windows for which matches must be found is N x M. Hence the amount of work increases with the square of the sequence length.
		If the sequences are not known to be homologous throughout their entire length, a local alignment should be the method of choice.
		Unless two sequences are known to be homologous over their entire length, a local alignment is preferable to a global alignment.
	helix.biology.mcmaster.ca /721/align.html (4730 words)

	Multiple Sequence and Structure Alignment in MOE (Site not responding. Last check: 2007-11-07)
		This alignment procedure is based upon the A* search algorithm (described in The A* Search and Applications to Sequence Alignment in this issue of the Journal of the Chemical Computing Group).
		Each sequence is removed from the collection aligned to the remaining sequences treating them as a single block; that is, we perform a 1-many alignment for each of the sequences in turn.
		The fundamental sequence alignment algorithm of MOE is capable of producing a pairwise alignment of two sequences given an arbitrary similarity matrix.
	www.chemcomp.com /feature/align.htm (1364 words)

	BSCI 348S - Pairwise Sequence Alignment
		Sequences from different organisms (or different loci) resemble each other primarily because they are homologous, and natural selection has conserved features of the sequence.
		Used when an objective and optimal measure is needed to compare two sequences and it is valid to assume that the length of the sequences is equivalent.
		The score of the sub-alignment is the sum of the partial alignment plus the BLOSUM score for the next two amino acids.
	www.life.umd.edu /labs/delwiche/bsci348s/lec/Align.html (904 words)

	Sequence Alignments (Site not responding. Last check: 2007-11-07)
		While ssearch reports only the best alignment between the query sequence and the library sequence, lalign and plalign will report a specified number of alignments (the default is 10) between the two sequences.
		lalign shows the actual local alignments between the two sequences and their scores, while plalign produces a plot of the alignments that looks similar to a `dot-matrix' homology plot.
		Sequences in the alignment are gathered into sub-groups on the basis of sequence similarity, functional similarity, or other criteria.
	www.rna.icmb.utexas.edu /linxs/seq-info/alignments.html (899 words)

	Instructions :: Mulan :: MUltple sequence Local AligNment and visualization tool
		The majority of the Mulan sequence analysis options correspond to the alignments of "finished"-quality sequences (sequences that are represented by a single contig).
		As schematically visualized on this diagram, multiple sequences will be automatically separated into blocks of homology and each of these blocks will be represented as a multiple sequence alignment independently of the order or orientation of the block-constructing subsequence from a particular species.
		Order or orientation of the sequences constructing a particular block does not matter, while the complete alignment is done in a matter that maximizes the total score through all the possible alignment blocks.
	mulan.dcode.org /mulanInstructions.php (1385 words)

	Bioinformatics, Computational Molecular Biology - Alignment, Strings, Sequences, Trees, Maps
		This is a good way to visualize the collection of all possible alignments of two strings and the grey-scale level indicates the degree of (un)certainty as to which is the correct or "true" alignment.
		between sequence alignment, compression and modelling of biological sequences, and alignment of non-random sequences.
		Allows alignments of two strings to be sampled at random from their posterior probability distribution.
	www.csse.monash.edu.au /~lloyd/tildeStrings (1848 words)

	MSA - Global Multiple Sequence Alignment Program Usage Guide
		would force positions 22 to 31 of sequence 2 to be aligned with positions 21 to 30 of sequence 3 and positions 25 to 34 of sequence 5; it would alse force position 35 of sequence 2 to be aligned with position 36 of sequence 3 and position 41 of sequence 5.
		The heuristic alignment is produced by using the consistant positions with all of the the pairwise alignments in conjunction with a progressive pairwise alignment technique across the inconsistant positions.
		Sequences that are greater than 300 residues will require a larger amount of memory to align.
	www.psc.edu /general/software/packages/msa/manual/manual.html (2466 words)

	Sequence Alignment References
		Allison, L., Wallace, C. and Yee, C. Finite-state models in the alignment of macromolecules.
		Rechid, R., Vingron, M. and Argos, P. A new interactive protein sequence alignment program and comparison of its results with widely used algorithms.
		Structural superposition of proteins with unknown alignment and detection of topological similarity using a six-dimensional search algorithm.
	cmgm.stanford.edu /biochem218/07AlignmentRefs.html (836 words)

	Sequences Alignments and Comparisons
		This form allows you to progressively load your sequences into a file, one by one, by re-using the loadseq program as long as the file is not complete.
		It's purpose is to help users who do not have a concatenate utility on their computer to build a multiple sequence file (HOWTO).
		protal2dna: Align DNA sequences corresponding to a protein alignment.
	bioweb.pasteur.fr /seqanal/alignment/intro-uk.html (285 words)

	Pairwise Alignment algorithms form
		When you want an alignment that covers the whole length of both sequences, use needle.
		When you are trying to find the best region of similarity between two sequences, use water.
		Sequence 1: paste Sequence in any format OR upload a file:
	www.ebi.ac.uk /emboss/align (61 words)

	BioEdit v7.0.5 General Information (Site not responding. Last check: 2007-11-07)
		BioEdit is a mouse-driven, easy-to-use sequence alignment editor and sequence analysis program designed and written by a graduate student who knows how frustrating and time consuming it can be to rely upon word-processors and command-line programs for sequence manipulation.
		BioEdit is intended to supply a single program that can handle most simple sequence and alignment editing and manipulation functions that researchers are likely to do on a daily basis, as well as a few basic sequences analyses.
		Sequences at least 4.6 Mb in length can be manipulated (the largest sequence tested so far is the E.
	www.mbio.ncsu.edu /BioEdit/page2.html (983 words)

	Dynamic Programming Tutorial (Site not responding. Last check: 2007-11-07)
		The first step in the global alignment dynamic programming approach is to create a matrix with M + 1 columns and N + 1 rows where M and N correspond to the size of the sequences to be aligned.
		Thus, the value for the cell at row 1 column 8 is the maximum of 1 (for a match), 0 (for a vertical gap) or 1 (horizontal gap).
		This means it looks to the neighbor to the left (gap in sequence #2), the diagonal neighbor (match/mismatch), and the neighbor above it (gap in sequence #1).
	www.sbc.su.se /~pjk/molbioinfo2001/dynprog/dynamic.html (944 words)

	SAM: UCSC's Sequence Alignment and Modeling System
		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.
		The alignment of each of a family to a trained model automatically yields a multiple alignment among those sequences.
	www.cse.ucsc.edu /research/compbio/sam.html (1181 words)

	SIM Alignment Tool - Protein Sequences
		SIM (References) is a program which finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence.
		Once the alignment is computed, you can view it using LALNVIEW, a graphical viewer program for pairwise alignments [references].
		These sequences may either be specified by their Swiss-Prot/TrEMBL accession numbers (AC), e.g.
	www.expasy.ch /tools/sim-prot.html (125 words)

	MegAlign (Site not responding. Last check: 2007-11-07)
		If you want to find more related sequences for alignment, simply run a BLAST query or utilize the Entrez text query interface, then drop in the sequences* you want from the list of matches.
		Differences in chemical, structural or functional characteristics between sequences can also be displayed as well as your own groupings or consensus.
		Bootstrapping is a process that compares trees generated from similar alignments and counts the number of times a specific branching pattern occurs.
	www.dnastar.com /web/r10.php (384 words)

	multiple sequence alignment: Interactive Editor STRAP
		Tue May 17: Also local alignment precedures can be used to align sequences.
		From the menu science multiple sequence alignment projects can be opened.
		structure based multiple sequence alignments of all pdb structures of all flavine proteins.
	www.charite.de /bioinf/strap (1136 words)

	New Services
		MAGEST for Maboya (the ascidian, Halocynthia roretzi) Gene Expression patterns and Sequence Tags is released as part of the Genome Databases in Japan.
		The sequence data are made available by the JST large-scale human genome sequencing projects.
		Human chromosome 21 sequence map by HGC was released.
	www.genome.ad.jp /WhatsNew/NewService.html (3860 words)

	PROTEIN SEQUENCE ANALYSIS - SEQUENCE ALIGNMENT (Site not responding. Last check: 2007-11-07)
		You might also be able to find an alignment at MIPS or in
		To explore your alignment further, click on View alignment in the PRINTS entry: this invokes the CINEMA alignment editor and its help file - use this to understand how the editor works.
		Enter the accession numbers (not ID codes) of your selected sequences into the input box provided, remembering to set the code in column 2 and set the output to PIR format.
	www.biochem.ucl.ac.uk /bsm/dbbrowser/c32/alignment.html (232 words)

	Tools for Multiple Alignments (Site not responding. Last check: 2007-11-07)
		Colour by amino acid physico-chemical property, similarity to consensus sequence, hydrophobicity or secondary structure.
		Alignments may be loaded from the PRINTS fingerprint database.
		A colour graphical interface to manually edit the alignment, and also to run dot-plot or Clustal W programs to locally improve the alignment.
	pbil.univ-lyon1.fr /alignment.html (403 words)

	alion: pairwise alignment (Site not responding. Last check: 2007-11-07)
		Please use the GCG programs GAP and BESTFIT or the NCBI program BLAST 2 Sequences for long alignments.
		Leave the sequences blank to try an example pair.
		Normalized and weighted gap penalties have the penalties normalized to the scoring matrix as above, but are also weighted based on the amino acid composition of the two sequences to account for compositional bias.
	dlb4.stanford.edu /alion (200 words)

	BCM Search Launcher: Multiple Sequence Alignments
		All sequences must be in the same format; See below for size/time limits.
		MSA: 8 sequences, 800 characters and 10 minutes.
		Please limit the Sequence Name to one line or less.
	searchlauncher.bcm.tmc.edu /multi-align/multi-align.html (196 words)

	BCM Search Launcher: Pairwise Sequence Alignment
		Cut and paste first sequence in Fasta format here:
		Cut and paste second sequence in Fasta format here:
		GAP2 - global DNA to cDNA alignment with GAP2 (MTU) [
	searchlauncher.bcm.tmc.edu /seq-search/alignment.html (145 words)

	IBIVU - Vrije Universiteit - Publications (Site not responding. Last check: 2007-11-07)
		Simossis V.A., Kleinjung, J. and Heringa J. (2005) Homology-extended sequence alignment.
		Simossis V.A. and Heringa J. (2004) The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods.
		Weljie A. and Heringa J. (2001) Sequence alignment of Ca-binding proteins.
	zeus.cs.vu.nl /publications (1055 words)

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