Sequence alignment
From MyBio
This listing include multiple sequence alignment tools, but the subcategories deal with pairwise sequence alignment, format conversion, tutorials, viewers and much more.
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JDotter is a platform-independent Java interactive user interface for the Linux version of Dotter - a widely used program for generating dot plots of DNA or protein sequences which is available at the Dotter homepage. JDotter runs as a client-server application; JDotter can send new sequences to the Dotter program for alignment as well as rapidly access a repository of pre-processed dot plots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. JDotter, therefore, greatly simplifies access to dot plot data and is especially useful in laboratories that deal with large numbers of genomes and/or have a multi-platform organization.
DNA Baser
Easy to use software package providing batch DNA sequence assembly, contig editing, chromatogram viewer and rapid detection of mutations in DNA sequences. It has a fast assembly engine with a range of features that greatly speeds the process of sequence assembly and mutation analysis. DNA Baser is the only software which allow batch assembly (it automatically scan a folder for samples that belongs to the same contig, based on a name pattern, and assemble those samples without users intervention). It can also 'assemble to reference'. The program is fully functional for 60 days.
Multiple alignment resource
VSNS BioComputing Division multiple alignment resource. Occasionally updated list of multiple alignment resources. Includes links to tools which both calculate and analyse multiple alignments.
Multalin
Multiple sequence alignment with hierarchical clustering. Multiple sequence alignment with hierarchical clustering F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890
ClustalW
Standard alignment tool. Clustal W is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms. New features include NEXUS and FASTA format output, printing range numbers and faster tree calculation.
ClustalW
EMBnet ClustalW web server.
DiAlign
Local sequence alignment for sequence of limited global similarity. DIALIGN is a novel program for multiple alignment developed by Burkhard Morgenstern et al. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing whole segments of the sequences. No gap penalty is used. This approach is especially efficient where sequences are not globally related but share only local similarities, as is the case with genomic DNA and with many protein families. DIALIGN has been found to be the best method for local multiple alignment.
ClustalW - GSA
Builds a multiple alignment of sequences (or sequence segments, accession numbers as entries) using CLUSTALW.
Consensus
Calculates the consensus for the CLUSTAL or MSF multiple alignment.
T-Coffee
Tree-based consistency Objective Function for alignment Evaluation. T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model. It also allows to estimate the level of consistency of each position within the new alignment with the rest of the alignments. T-Coffee Replaces The COFFEE objective function that had been implemented in SAGA. Please, note that COFFEE will not be maintained anymore in SAGA.
QAlign
Multiple alignment and editor using DCA, CLUSTAL-W, T-COFFEE, and DIALIGN. QAlign provides a practical solution for the creation of high-quality multiple alignments: layouts produced by automated methods may be used as a starting-point for manual changes, whereas the phylogenetic consequences are visualized on the fly. The standalone software package combines various alignment algorithms with a versatile editor and a dynamic phylogenetic analysis to provide a convenient graphical user interface. In addition to the traditional alignment strategies of fast progressive (Clustal W) and more accurate simultaneous multiple alignment (DCA), QAlign includes iterative and consistency-based state-of-the-art extensions, which recently have shown much promise (T-coffee and DIALIGN). Thus, after providing the input sequences (FASTA and MSF format) and selecting the evolutionary model (PAM, BLOSUM, DNA/RNA), the user may choose from a list of strategies/algorithms that one which suits the problem best. However, even these layouts may need some manual editing. Therefore, the graphical editor of QAlign provides all features needed to support convenient editing. A dynamical consensus is updated on every edit event, visualizing the strength of each character in an easy coloring scheme. Furthermore, a phylogenetic analysis of the current alignment layout is created interactively (using the neighbor-joining method), which may be refined (e.g. by applying bootstrapping techniques) and exported (NEWICK and SVG or WMF vector-format).
MGAlignIt
Web service for the alignment of mRNA/EST and genomic sequences. MGAlign is a novel, rapid, memory efficient and practical method for aligning mRNA/EST and genome sequences. Allows users to effectively visualize the alignment in a graphical manner and to perform limited analysis on the alignment output. The server also permits the alignment to be saved in several forms, both graphical and text, suitable for further processing and analysis by other programs.
(Multi)PipMaker
PipMaker aligns two DNA sequences and returns a percent identity plot of that alignment, together with a traditional textual form of the alignment. MultiPipMaker server, which aligns multiple, long genomic DNA sequences quickly and with good sensitivity. Alignments are computed between a contiguous reference sequence and one or more secondary sequences, which can be finished or draft sequence. The outputs include a stacked set of percent identity plots, called a MultiPip, comparing the reference sequence with subsequent sequences, and a nucleotide-level multiple alignment. Tools are provided to search MultiPipMaker output for conserved matches to a user-specified pattern and for conserved matches to position weight matrices that describe transcription factor binding sites (singly and in clusters). Analysis of the alignments also confirms the phylogenetic inference that horses are more closely related to cats than to cows.
VISTA Browser
Align and detect conserved regions in long genomic sequences.
SIM4
SIM4 addresses the problem of efficiently aligning a transcribed and spliced DNA sequence (mRNA, EST) with a genomic sequence containing that gene, allowing for introns in the genomic sequence (taking.
Genome VISTA
Align a sequence to its ortholog in the human genome.
Stretcher
Global alignment between two sequences which includes percentage identity.
Spidey
Spidey is an mRNA-to-genomic alignment program.
CHAOS DIALIGN
CHAOS is used to rapidly identify strong sequence similarities that serve as anchor points to speed-up the DIALIGN alignment procedure.
FMAP
Map your sequence to Human genome draft for a second.
JALI
Jumping Alignments. This program takes as input a protein sequence and a multiple alignment of a protein family and computes a jumping alignment of the sequence and the alignment.
FLAG
Fast Local Alignment of Gigabases. Incorporates (1) Pairwise Flag: Performing local alignment of two DNA sequences, especially powerful for long-sequence comparison(e.g. > 500 kb), (2) Cluster Flag: A Genbank searching tool based on local alignment of nucleotide sequences, and (3) Protein Flag: A protein database searching tool based on local alignment of protein sequences
Pfam
Allows sequence search against protein families database of alignments and HMMs
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Wise2
Align a protein or profile HMM against genomic sequence to predict a gene structure, and related tools.
DCA
Divide-and-Conquer Multiple Sequence Alignment.
AMAS
Analyse Multiply Aligned Sequences. AMAS is a program to analyse multiple alignments of protein sequences. It allows the identification of functional residues by comparison of sub-groups of sequences arranged on a tree.
MAVID
Multiple alignment server. MAVID is a multiple alignment program suitable for many large genomic regions. The MAVID web server allows biomedical researchers to quickly obtain multiple alignments for genomic sequences and to subsequently analyse the alignments for conserved regions. MAVID has been successfully used for the alignment of closely related species such as primates and also for the alignment of more distant organisms such as human and fugu. The server is fast, capable of aligning hundreds of kilobases in less than a minute. The multiple alignment is used to build a phylogenetic tree for the sequences, which is subsequently used as a basis for identifying conserved regions in the alignment.
Lagan Toolkit
The Lagan Tookit is a set of alignment programs for comparative genomics. The three main components are a pairwise aligner (LAGAN), a multiple aligner (M-LAGAN), and a glocal aligner (Shuffle-LAGAN). All three are based on the CHAOS local alignment tool and combine speed (regions up to several megabases can be aligned in minutes) with high accuracy. The results of the alignment can be visualized using the VISTA visualization tool.
Alces
Inside Site: Physical Map. Chromosome R.. Chromosome 1. Chromosome 2. Chromosome 3. Chromosome 4. Chromosome 5. Chromosome 6. Chromosome 7. SNP Map. Contact Information. Additional Links: Candida Genome Database. Stanford. Assembly 19. ...
Multiple Sequence Alignment - CLUSTALW
ClustalW Multiple Sequence Alignment web server at Kyoto University ICR's Bioinformatics Center
TSDA
TargetSiteDuplicationAlign. TSDA is an alignment tool to analyze recombinant DNA sequences. The program calculates (local) similarity of two sequences and shows the optimal alignment(s). The development was done using the algebraic dynamic programming (ADP) method.
YASS : DNA local alignment program
YASS is a DNA local alignment tool that use several transition constrained seeds to increase its sensitivity/selectivity ratio. Results can be directely shown as dotplots.
MAFFT alignment and NJ / UPGMA phylogeny
Multiple sequence alignment by MAFFT. MAFFT offers a range of multiple alignment strategies, L-INS-i (accurate; recommended for <200 sequences), FFT-NS-i (standard speed and accuracy), FFT-NS-2 (fast; recommended for >2,000 sequences)
AliWABA: ALIgnment With ABA
AliWABA is a website and portal for ABA, the A-Bruijn Aligner described in:. A Novel Method for Multiple Alignment of Sequences with Repeated and Shuffled Elements. Benjamin Raphael, Degui Zhi, Haixu Tang, and Pavel Pevzner. Genome ...
