User:Wayne Decatur/Sequence analysis tools

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1 Have not Categorized Yet
2 Converters
3 Random sequence generators
4 Sequence shufflers
5 Some sequence analysis but mostly OTHER
6 Good E. coli database
7 NGS
8 Nucleic acid system building
- 8.1 ===========
- 8.2 =================================

Have not Categorized Yet

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
PrePPI: database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human.

Converters

ALTER (ALignment Transformation EnviRonment) - complex interface but offers lots of options for output. I used it as part of my workflow to get closer to special NEXUS format (or intermediate) for performing maximum likelihood phylogenetic analysis of large sets of sequences.
Sequence conversion Provided by bugaco.com - a lot of conversion choices with easy interface. When I had interleaved clustal format it converted nicely to a straight fasta listing for the sequence for every organism.

Random sequence generators

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.