> > Mapping and Assembly

Mapping and Assembly

This section contains links to mapping data, contig assembly, and genome resources used by many genome sequencing projects.

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Found 16 links

Displaying 15 links

CAP3 Sequence Assembly ProgramTool Content

http://bioweb.pasteur.fr/seqanal/interfaces/cap3.html

DNA > Mapping and Assembly

Web-based contig assembly.

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tagsalgorithms bacterial chromosomes consensus sequence contig mapping dna sequence analysis factual databases genetic models reproducibility of results sequence alignment theoretical models

eBioinformaticsResource Content

http://www.ebioinformatics.org/

DNA > DNA and Genomic Analysis
DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Presentation and Format
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3.

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EGassemblerTool Content

http://egassembler.hgc.jp

DNA > Mapping and Assembly
Expression > cDNA, EST, SAGE

EGassembler is a pipeline for clustering and assembling sequence fragments from transcript (EST) data or from shotgun sequencing.

This content is being maintained by amasoudin.

NAR Web Server Issue 2006
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tagscomputational biology dna sequence analysis expressed sequence tags genomics

Genome Centres and DatabasesResource Content

http://www.ncbi.nlm.nih.gov/genomes/static/links.html

DNA > Mapping and Assembly
Human Genome > Other Resources
Model Organisms > General Resources

Genome centers and databases listed by organism.

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Genome Database for RosaceaeDatabase Content

http://www.rosaceae.org/

DNA > Mapping and Assembly
Expression > cDNA, EST, SAGE
Model Organisms > Plants

Genome Database for Rosaceae (GDR) contains all publically available Rosaceae sequences including annotated peach, strawberry and almond EST sequences and the genetically anchored peach physical map.

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tagschromosome mapping expressed sequence tags genetic databases genetic markers genetics genomics plant genome research rosaceae sequence alignment systems integration

HapEditTool Content

http://embio.yonsei.ac.kr/hapedit

DNA > Mapping and Assembly

HapEdit is a tool for assessing the accuracy of assembled haplotypes. Editting functions such as breaking erroneous haplotype segments into smaller segments or concatenating haplotype segments are also possible.

NAR Web Server Issue 2011
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iCE - internet Contig ExplorerTool Content

http://www.bcgsc.ca/platform/bioinfo/software/ice

DNA > Mapping and Assembly
Model Organisms > General Resources

Viewer for physical map data (for mouse, rat, cow, Cryptococcus); developed at the Genome Sciences Centre, Vancouver.

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tagsanimals arabidopsis caenorhabditis caenorhabditis elegans contig mapping dna fingerprinting helminth dna humans mice molecular cloning oryza sativa plant dna rats

MagicViewerTool Content

http://bioinformatics.zj.cn/magicviewer/

DNA > Annotations
DNA > Mapping and Assembly
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Sequence Polymorphisms

MagicViewer allows easy visualization of short read mapping, and identification and annotation of genetic variation using next-generation sequencing data. Platforms covered include Roche 454, ABI SOLiD and Illumina.

NAR Web Server Issue 2010
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tagsgenetic variation genomics indel mutation sequence alignment sequence analysis single nucleotide polymorphism systems integration

MGIPTool Content

http://mgip.biology.gatech.edu

DNA > Mapping and Assembly
Human Genome > Health and Disease
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics
Sequence Comparison > Pairwise Sequence Alignments

The Meningococcus Genome Informatics Platform (MGIP) is a suite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize the specific sequence type and clonal complex of the Neisseria meningitidis strain.

NAR Web Server Issue 2009
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tagsalleles bacterial genome bacterial typing techniques dna sequence analysis genomics neisseria meningitidis reproducibility of results

NCBI Clone RegistryDatabase Content

http://www.ncbi.nlm.nih.gov/genome/clone/

DNA > Mapping and Assembly

A database that integrates information about genomic clones and libraries, including sequence data, genomic position, and distributor information.

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setsNational Center for Biotechnology Information (NCBI)

Phred/Phrap/Consed SystemTool Content

http://www.phrap.org/phredphrapconsed.html

DNA > Mapping and Assembly

UNIX-based, base-calling, sequence assembly and finishing tools used by most genome sequence centres; free for non-commercial use.

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Projector 2Tool Content

http://molgen.biol.rug.nl/websoftware/projector2/

DNA > Mapping and Assembly
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

Projector 2 allows users to map completed portions of the genome sequence of an organism onto the finished (or unfinished) genome of a closely-related species or strain. Using the related genome sequence as a template can facilitate sequence assembly and the sequencing of the remaining gaps.

NAR Web Server Issue 2005
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tagsalgorithms bacterial genome contig mapping dna primers genomics polymerase chain reaction

PromoSerTool Content

http://biowulf.bu.edu/zlab/PromoSer/

DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection

Server which aims to extract proximal promoter sequences from mammalian genomes. Does so by mapping mRNA and EST sequences and tracking overlapping alignments to find the transcription start site.

NAR Web Server Issue 2004NAR Web Server Issue 2003
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tagsalgorithms animals dna sequence analysis expressed sequence tags genetic promoter regions genome humans messenger rna mice oligonucleotide array sequence analysis rats rna sequence analysis sequence alignment sequence analysis transcription initiation site

TIGR Software ToolsResource Content

http://www.tigr.org/software/

DNA > Annotations
DNA > Gene Prediction
DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection
Expression > Transcript Expression Analysis
Sequence Comparison > Comparative Genomics

A list of open-source software packages available for free from The Institute for Genomic Research (TIGR).

NAR Web Server Issue 2003
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tagsarabidopsis dna sequence analysis eukaryotic cells exons genes introns markov chains plant genes

TmPrimeTool Content

http://prime.ibn.a-star.edu.sg

DNA > Mapping and Assembly
DNA > Tools For the Bench

TmPrime allows users to design oligonucleotide sets for gene assembly by both ligase chain reaction and polymerase chain reaction. The program also provides functions to separate long genes into smaller fragments for multi-pool assembly and codon optimization for expression.

NAR Web Server Issue 2009
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tagsdna sequence analysis humans ligase chain reaction oligonucleotides polymerase chain reaction proteins synthetic genes

Tags associated with subcategory 'DNA/Mapping and Assembly'

dna sequence analysis algorithms genomics humans sequence alignment contig mapping animals molecular cloning expressed sequence tags mice systems integration computational biology genetic promoter regions messenger rna genome rna sequence analysis oligonucleotide array sequence analysis genetic predisposition to disease genetic linkage inborn genetic diseases thyroid neoplasms sequence analysis polymerase chain reaction dna primers factual databases transcription initiation site caenorhabditis molecular sequence data caenorhabditis elegans dna fingerprinting plant dna oryza sativa helminth dna genomic library database management systems gene expression profiling data display computing methodologies genetic databases restriction mapping time factors sequence tagged sites sensitivity and specificity genes nucleic acid sequence homology open reading frames high-throughput screening assays drosophila melanogaster indel mutation single nucleotide polymorphism introns exons eukaryotic cells chromosome mapping arabidopsis plant genome genetics genetic markers research rosaceae National Center for Biotechnology Information (NCBI) base sequence genetic variation markov chains plant genes amino acid sequence homology theoretical models reproducibility of results complementary dna computer systems rats gene expression regulation escherichia coli genetic models consensus sequence proteins oligonucleotides ligase chain reaction synthetic genes alleles bacterial chromosomes neisseria meningitidis bacterial typing techniques bacterial genome