User:Wayne Decatur/Sequence analysis tools

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Revision as of 20:58, 21 July 2015

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.
• Three to One converts three letter amino acid sequence translations to single letter translations.
• One to Three converts single letter amino acid sequence translations to three letter translations.

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.

My own sequence work-related code

• [1]
• Working with UGENE software analysis software

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."

Fungal Genome Resources

http://fungalgenomes.org/

http://1000.fungalgenomes.org/home/

http://fungidb.org/fungidb/ (about it –> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245123/)

http://genome.jgi.doe.gov/programs/fungi/1000fungalgenomes.jsf <— nice graphic of situation related to 1000 fungal genomes project

http://genome.jgi-psf.org/programs/fungi/index.jsf

http://www.broadinstitute.org/scientific-community/science/projects/fungal-genome-initiative/fungal-genomics

http://fungi.ensembl.org/index.html

http://en.wikipedia.org/wiki/List_of_sequenced_fungi_genomes <– how current is it???

For genomic arrangement (synteny) comparisons/Fungal Genomics Resources

Synteny Viewer listed under every SGD gene on Sequence tab, near bottom of page

http://www.genomicus.biologie.ens.fr/genomicus-fungi-19.01/cgi-bin/search.pl

[Yeast Gene Order Browser (YGOB)] (http://ygob.ucd.ie/)