User:Wayne Decatur/Sequence analysis tools

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BLAST+


Circos


Converters

Random sequence generators

Sequence shufflers


Orthology

  • EggNOG - A database of orthologous groups and functional annotation


Pattern Matching


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)


RNA Structure Analysis

Sequence Logo Generation

Installable software for fine-tuning sequence alignments

Windows equivalent is here but I have NOT tried it.

Python-based utilities

  • seqmagick-An imagemagick-like frontend to Biopython SeqIO. For example, it can convert from fasta to phylip, remove gaps from a fasta-formatted sequence, and describe all FASTA files in the current directory. Requires Biopython.
  • see also on this page 'Binder'-related items as I usually have provided a way to shuttle other command-line based software output to Python

My own sequence work-related code

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur

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