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CCB Bioinformatics EMBOSS Pipeline Workflows
Overview
This page contains a number of bioinformatics workflows based on the advanced EMBOSS informatics package. This page describes as Pipeline modules several bioinformatics tools from the EMBOSS suite and demonstrates the construction of a couple of integrated pipeline workflows (end-to-end bioinformatics solutions via the LONI Pipeline).
Problems addressed by EMBOSS workflows
The most popular EMBOSS applications include:
| Program group | Selected applications |
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| Alignment | Local (matcher, water) and global (stretcher, needle) alignment |
| Coding regions | Synonymous codon use (syco), codon statistics (chips) |
| Comparison | Large sequence word comparisons (dottup, polydot, wordmatch) and alignment (supermatcher) |
| Composition | General (compseq), frequent words (wordcount), graphical representation (chaos) |
| CpG? islands | Report (cpgreport) and plot (cpgplot) |
| DNA features | Repeats (einverted, etandem), DNA melting (dan) |
| Editing | General editing utilities (cutseq, splitter), features (maskfeat), etc. |
| Indexing | Database indexing (dbiflat, dbigcg, dbiblast) |
| Motifs | Searching prosite (patmatdb, motifsearch), prints (pscan), transfac (tfscan), general patterns (fuzznuc, fuzzpro) |
| Multiple alignment | Interface to clustalw (emma), display (prettyplot), editing (mse) |
| Protein features | Functional motifs (antigenic, sigcleave), structural motifs (pepcoil, helixturnhelix), amphipathic regions (pepnet, pepwheel), transmembrane prediction (tmap) and display (topo) Protein properties Hydropathy (pepwindow, pepwindowwall, octanol), protease sites (digest), general (pepstats) |
| Sequence formats | Sequence reading/writing/format conversion (seqret, seqretall) and feature format conversion (seqretfeat) |
| Translation | Codon usage (cusp), reading frames (getorf, showorf, backtranseq) |
| Utilities | Motif database indexing (rebaseextract, tfextract, prosextract, printsextract), listing databases (showdb), searching for applications (wossname) |
Detailed Workflow Usage & Specifications
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Chips: This tool computes the Codon usage statistics. Chips calculates Frank Wright's Nc statistic for the effective number of codons used.
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Matcher Finds the best local alignments between two sequences. It can be used to compare two sequences looking for local sequence similarities using a rigorous algorithm. Matcher is based on Bill Pearson's 'lalign' application, version 2.0u4 Feb. 1996.
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EBOSS LONI Installation
The LONI EBOSS installation needs to be provisioned to /usr/local (by the LONI IT team). The current test installation is in:
- /ifs/ccb/CCB_SW_Tools/others/Bioinformatics/EMBOSS_6_2010/EMBOSS-6.3.1/ and Pipelines folder.
- See the README file for configuration, build, test and validation instructions.
Footnotes
- Outputs and results:
- Expected times:
- Limitations:
- Contact person/group: SIG-FLOW Team
- Pubs: Publications
- Grants
- Tools/packages used in this workflow:
- Notes
EMBOSS References
See also
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