Software Tools :: Software by Function
The Center for Genomics and Bioinformatics provides access to a variety of software and database services, some
of which are available at no charge to the research community (e.g., EMBOSS,
PHYLIP) and some of which are provided free of charge to the IU community
(e.g., GCG, SeqLab, TRANSFAC)
The available tools are broken down into several categories.
Finding the right tool is simple; pick a category to match the analysis you're
interested in. The subsequent page will provide documentation, notes, and
links to specific sequence analysis programs to assist you.
| Sequence Creation and Manipulation |
Create and edit sequence files
- edit sequences
- shuffle, corrupt, mask sequences
- complement, reverse-complement nucleic acid sequences
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| Mapping and Digests
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Find cut sites and digestion fragments
- restriction enzyme cut sites and fragments
- proteolytic enzyme cut sites and fragments
- protein isoelectric points
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| Format conversions -- sequences and other files
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Convert files from one format to another
- sequence files
- scoring matrix files
- restriction enzyme files
- profile files
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| Motifs, patterns, and profiles
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Find motifs, patterns, and domains in sequences
- simple sequence patterns
- functional sites or domains
- profiles/HMMs representing a sequence family
- MEME (Multiple Expectation maximization for Motif Elicitation)
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| Translations
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Convert sequences from one type to another
- translate DNA/RNA to protein
- reverse translate protein to DNA/RNA
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| Gene finding and codon analysis
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Locate potential genes and exons in nucleic acid sequences; find regions of codon bias
- search by content -- ORF analysis, codon bias, ...
- search by signal -- promoters, intron/exon boundaries, ...
- search by homology -- locate ESTs on genomic sequences, ...
- combination approaches -- TESTCODE, Markov models, ...
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Database reference search
Database similarity search
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Find sequences of interest in a database by searching the annotation section of database entries with
keywords
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DNA sequence assembly
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Assemble nucleic acid sequences from overlapping fragments
- trace file viewers
- sequence fragment preprocessing
- sequence assembly project management
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Sequence alignments and comparisons
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Align two or more sequences
- pair-wise global and local alignments
- multiple sequence alignments
- information about sequence alignments
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Phylogenetic analysis
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Create phylogenetic trees from sequence data
- distance matrix methods, neighbor joining
- parsimony methods
- maximum likelihood methods
- synonymous vs nonsynonymous substitutions
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Primers and probes
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Find PCR or sequencing primers; find hybridization probes
- primer and probe candidates
- primer pair compatibility for PCR
- oligonucleotide melting temperatures
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Information engineering in biology
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Programming, web services, and databases
- Perl, Python, Java programming; Bio projects
- XML, DAS, GEML, MAML data annotation formats
- Gene Ontology Consortium
- web services (CGI, servlets, CORBA)
- databases, information systems, data mining
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RNA secondary structure analysis
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Predict RNA folding; find inverted and tandem repeats in nucleic acid sequences
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Protein sequence analysis
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Examine protein features and properties; determine secondary and tertiary structure
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