> > Other Alignment Tools

Other Alignment Tools

Tools for aligning sets of sequences to a reference sequence (for example, cDNA to genomic).

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ASPicTool Content

http://t.caspur.it/ASPIC/

Expression > Splicing
Expression > cDNA, EST, SAGE
Sequence Comparison > Other Alignment Tools

Alternative Splicing Prediction (ASPic) can predict alternative splicing of user submitted genes based on comparative analysis of available transcript and genome data from a variety of species. Results include graphical and tabular views of the splicing patterns of full-length mRNA isoforms compatible with the detected splice sites of the genes as well as structural and functional annotations.

NAR Web Server Issue 2006
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tagsalgorithms alternative splicing animals base sequence benchmarking exons gene expression profiling genomics heterogeneous-nuclear ribonucleoproteins humans introns messenger rna molecular computers molecular models protein isoforms rna splice sites sequence alignment software design software validation

E2GTool Content

http://bibiserv.techfak.uni-bielefeld.de/e2g/

Expression > cDNA, EST, SAGE
Sequence Comparison > Other Alignment Tools

E2G is a tool that maps a large set of EST and cDNA sequences to a user-supplied genomic sequence. The use of pre-computed indexed data structures increases the efficiency of the sequence comparison process, allowing a large amount of data to be mapped within a reasonable timeframe.

NAR Web Server Issue 2004
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tagsbase sequence chromosome mapping complementary dna expressed sequence tags genomics sequence alignment

Genotyping - NCBITool Content

http://www.ncbi.nih.gov/projects/genotyping/formpage.cgi

Model Organisms > Other Organisms
Sequence Comparison > Other Alignment Tools

The Genotyping tool at the NCBI identifies the genotype (or subtype) of viral sequences by using a sliding window approach to BLAST analysis against reference sequences for different viral subtypes. Results are shown as a graphical output plotting the top-scoring genotype. An alignment tool is also available.

NAR Web Server Issue 2004
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tagsalgorithms dna sequence analysis genetic recombination genotype hepacivirus hepatitis b virus hiv-1 molecular sequence data sequence alignment viral dna viral genes viral genome viruses
setsNational Center for Biotechnology Information (NCBI)

HHrepTool Content

http://toolkit.tuebingen.mpg.de/hhrep

Protein > 2-D Structure Prediction
Protein > Sequence Features
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

HHrep is a tool for the de novo identification of repeats in protein sequences based on the pairwise comparison of profile hidden Markov models (HMMs).

NAR Web Server Issue 2006
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tagsamino acid repetitive sequences markov chains protein folding protein sequence analysis sequence alignment

HMMER Web ServerTool Content

http://hmmer.janelia.org

Protein > Sequence Comparison
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

HMMER Web Server is a tool for interactive sequence similarity searching. Methods are available for single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence databases, and for searching a protein sequence against Pfam.

NAR Web Server Issue 2011
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IccareTool Content

http://genopole.toulouse.inra.fr/bioinfo/Iccare/

Sequence Comparison > Other Alignment Tools

The Iccare (Interspecific Comparative Clustering and Annotation foR Est) web server compares all available EST and mRNA sequences for a query organism against the set of transcripts for a reference organism. The results are presented graphically and relative to the location of genes on the chromosomes of the reference organism.

NAR Web Server Issue 2004
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tagsanimals arabidopsis chromosome mapping dna primers dna sequence analysis expressed sequence tags human genome humans messenger rna nucleic acid databases nucleic acid probes nucleic acid sequence homology plant genes rna sequence analysis rna splice sites systems integration

IMGT/V-QUESTTool Content

http://imgt.cines.fr/

Sequence Comparison > Other Alignment Tools

The international ImMunoGeneTics information system (IMGT) V-QUEry and STandardization (V-QUEST) tool compares a user-provided fasta-formatted germline or rearranged T cell receptor or immunoglobulin variable sequence with a reference set of sequences.

NAR Web Server Issue 2004NAR Web Server Issue 2008
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tagsalgorithms animals b-lymphocyte gene rearrangement dna sequence analysis humans immunoglobulin fragments immunoglobulin genes immunoglobulin joining region immunoglobulin variable region mice rats sequence alignment systems integration t-lymphocyte gene rearrangement

MaxAlignTool Content

http://www.cbs.dtu.dk/services/MaxAlign/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Other Alignment Tools

MaxAlign is a web server for maximizing usable data in an alignment. It maximizes the number of nucleotide (or amino acid) symbols present in gap-free columns by selecting the optimal subset of sequences to exclude from the alignment.

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tagsalgorithms automated pattern recognition genetic databases sequence alignment sequence analysis

PAL2NALTool Content

http://coot.embl.de/pal2nal/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Other Alignment Tools

PAL2NAL converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. Synonymous (Ks) and non-synonymous (Ka) substitution rates can be calculated.

NAR Web Server Issue 2006
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tagscodon dna sequence analysis exons protein sequence analysis sequence alignment

SIM4Tool Content

http://pbil.univ-lyon1.fr/sim4.php

Sequence Comparison > Other Alignment Tools

Align cDNA with genomic DNA, allowing for introns and small number of sequencing errors.

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tagsalgorithms animals complementary dna computational biology dna drosophila melanogaster expressed sequence tags genome humans messenger rna mice nucleic acid sequence homology sequence alignment

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

Wise2Tool Content

http://www.ebi.ac.uk/Wise2/

Sequence Comparison > Other Alignment Tools

The Wise2 form compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.

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Tags associated with subcategory 'Sequence Comparison/Other Alignment Tools'

sequence alignment algorithms humans dna sequence analysis messenger rna animals expressed sequence tags genomics base sequence consensus sequence computer simulation evaluation studies as topic factual databases systems integration fibronectins dna primers chromosome mapping human genome nucleic acid databases rna splice sites plant genes nucleic acid probes molecular sequence data genes computational biology complementary dna dna drosophila melanogaster nucleic acid sequence homology mice genome sensitivity and specificity rna sequence analysis protein conformation phylogeny genetic models protein databases protein sequence analysis reproducibility of results proteins protein-serine-threonine kinases t-lymphocyte gene rearrangement rats sequence analysis genetic databases automated pattern recognition markov chains protein folding hepatitis b virus hepacivirus rna splicing amino acid sequence homology amino acid sequence genetic recombination codon amino acid repetitive sequences genotype alternative splicing amino acid motifs arabidopsis b-lymphocyte gene rearrangement hiv-1 National Center for Biotechnology Information (NCBI) software design protein isoforms molecular models software validation immunoglobulin fragments immunoglobulin variable region immunoglobulin joining region immunoglobulin genes molecular computers introns viral genome viral genes viral dna viruses benchmarking heterogeneous-nuclear ribonucleoproteins gene expression profiling exons