User:Wayne Decatur/Sequence analysis tools
From Proteopedia
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* [http://nucleobytes.com/index.php/ Nucleobytes] - DNA editor and [http://nucleobytes.com/index.php/4peaks 4peaks] sequence chromatogram viewer along with other mac software | * [http://nucleobytes.com/index.php/ Nucleobytes] - DNA editor and [http://nucleobytes.com/index.php/4peaks 4peaks] sequence chromatogram viewer along with other mac software | ||
*[http://pax-db.org/#!home PaxDb]: Protein Abundance Across Organisms | *[http://pax-db.org/#!home PaxDb]: Protein Abundance Across Organisms | ||
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| + | Random sequence generators: | ||
| + | * http://users-birc.au.dk/biopv/php/fabox/random_sequence_generator.php | ||
| + | * http://www.bioinformatics.org/sms2/random_dna.html | ||
| + | * http://www.faculty.ucr.edu/~mmaduro/random.htm | ||
| + | * http://molbiol.ru/eng/scripts/01_16.html | ||
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| + | Sequence shufflers: | ||
| + | * http://emboss.sourceforge.net/ - shuffleseq from EMBOSS shuffles a set of sequences maintaining composition. | ||
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NGS: | NGS: | ||
* [http://homer.salk.edu/homer/basicTutorial/genomeBrowsers.html HOMER] - "Software for motif discovery and next-gen sequencing analysis". Nice in that it actually explains some of the details and advantages of the browsers and file types. | * [http://homer.salk.edu/homer/basicTutorial/genomeBrowsers.html HOMER] - "Software for motif discovery and next-gen sequencing analysis". Nice in that it actually explains some of the details and advantages of the browsers and file types. | ||
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| + | Nucleic acid system building: | ||
| + | * [http://www.nupack.org/ NUPACK] - "NUPACK is a growing software suite for the analysis and design of nucleic acid systems." | ||
Revision as of 16:30, 3 July 2014
- Plasmapper
- Online Schematic plasmid drawing tool
- Online restriction mapper
- NEBcutter
- old web cutter
- Sequence Manipulation Suite: Restriction Map - has at the left side links to other tools they have
- Biotools and EMBOSS at UMASS MED
- MUSCLE: MUltiple Sequence Comparison by Log-Expectation
- Archaeopteryx for the visualization of annotated phylogenetic trees.
- Netprimer
- Genomicus: Genomes in Evolution - "genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologically along evolutionary time."
- SeqTrace- "is an application for viewing and processing DNA sequencing chromatograms (trace files). SeqTrace makes it easy to quickly generate high-quality finished sequences from a large number of trace files. SeqTrace can automatically identify, align, and compute [contig] consensus sequences from matching forward and reverse traces, filter low-quality base calls, and perform end trimming of finished sequences. The finished DNA sequences can then be exported to common sequence file formats, such as FASTA. " Written in Python.
- CAP3 Sequence Assembly Program - online, webserver for making contigs from DNA sequences. "form allows you to assemble a set of contiguous sequences (contigs) with the CAP3 program.
- Nucleobytes - DNA editor and 4peaks sequence chromatogram viewer along with other mac software
- PaxDb: Protein Abundance Across Organisms
Random sequence generators:
- http://users-birc.au.dk/biopv/php/fabox/random_sequence_generator.php
- http://www.bioinformatics.org/sms2/random_dna.html
- http://www.faculty.ucr.edu/~mmaduro/random.htm
- http://molbiol.ru/eng/scripts/01_16.html
Sequence shufflers:
- http://emboss.sourceforge.net/ - shuffleseq from EMBOSS shuffles a set of sequences maintaining composition.
Some sequence analysis but mostly other
- BioCyc Database Collection - "BioCyc is a collection of 3530 Pathway/Genome Databases (PGDBs), with tools for understanding their data. Cellular Overview image generated by Pathway Tools. Explore Metabolic Maps for Thousands of Organisms. RouteSearch: Search for Paths through the Metabolic Network. Cross-Organism Search form generated by Pathway Tools. New: Search All of BioCyc for Genes, Proteins, Pathways. Search all of BioCyc or designated taxonomic groups for named genes, proteins, metabolites, pathways. Multiple Sequence Alignment results generated by Pathway Tools using MUSCLE. PatMatch query and results by Pathway Tools. SmartTable display generated by Pathway Tools. Metabolomics Data Analysis. Cellular Overview Omics Viewer image generated by Pathway Tools. Gene Expression Data Analysis. Multi-Genome Browser. Comparative Genome Analysis."
Good E. coli database:
- - EcoProDB E. coli protein database (EcoProDB) integrates protein information identified on 2-D gels along with other resources to provide the comparative platform for the expression levels of many heterogeneous proteins under different genetic and environmental conditions using the interactive interface and search mechanism.
NGS:
- HOMER - "Software for motif discovery and next-gen sequencing analysis". Nice in that it actually explains some of the details and advantages of the browsers and file types.
Nucleic acid system building:
- NUPACK - "NUPACK is a growing software suite for the analysis and design of nucleic acid systems."
