Other Alignment Tools

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

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Displaying 15 links

ASPicTool Content

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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.

BWATool Content

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Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates.

E2GTool Content

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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.

Genotyping - NCBITool Content

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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.

links directory index: 98
TitlePublication YearGoogle Scholar Citation Count
A web-based genotyping resource for viral sequences200498

HHrepTool Content

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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).

This content is being maintained by Johannes Soeding.

HMMER Web ServerTool Content

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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.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
HMMER web server: interactive sequence similarity searching201124

IccareTool Content

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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.

MaxAlignTool Content

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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.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
MaxAlign: maximizing usable data in an alignment20079

mrsFAST-UltraTool Content

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mrsFAST-Ultra is designed to map short reads to reference genome assemblies; in a fast and memory-efficient manner.

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PAL2NALTool Content

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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.

PASSTool Content

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PASS has been developed with an innovative strategy to perform fast gapped and ungapped alignment onto a reference sequence. It supports several data formats and allows the user to modulate very finely the sensitivity of the alignments. The program is designed to handle huge amounts of short reads generated by Solexa, SOLiD and Roche-454 technology. PASS is useful for single read mapping, paired-end resequensing, small RNA discovery and RNA-seq mapping.

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SegemehlTool Content

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segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to map primer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA).

SHORETool Content

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SHORE, for Short Read, is a mapping and analysis pipeline for short DNA sequences produced on a Illumina Genome Analyzer. It is designed for projects whose analysis strategy involves mapping of reads to a reference sequence. This reference sequence does not necessarily have to be from the same species, since weighted and gapped alignments allow for accuracy even in diverged regions.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count