User:Konrad U Foerstner/Tools and procedures: Difference between revisions
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* [http://www.genome.jp/kegg/mapper.html KEGG Mapper] (untested) | * [http://www.genome.jp/kegg/mapper.html KEGG Mapper] (untested) | ||
== | == Transcription Terminator prediction == | ||
* [http://transterm.cbcb.umd.edu/ TransTerm] | * [http://transterm.cbcb.umd.edu/ TransTerm] | ||
== miRNA target prediction == | |||
[[http://cegg.unige.ch/mirmap/]] (untested) | |||
== Python == | == Python == | ||
Revision as of 05:43, 18 December 2012
SNP calling
With Samtools
- Important. Base alignment quality (BAQ) is switched on per default and very (too) strict 5 Things to Know About SAMtools Mpileup
Phylogenetic trees
Multiple alignments
TSS prediction
- TSSi (untested)
Whole genome alignments
Pathway visualization
- iPath2.0 (by Takuji!) - the modified and original maps can be downloaded as SVG (e.g. full metabolic map)
- KEGG Mapper (untested)
Transcription Terminator prediction
miRNA target prediction
[[1]] (untested)
Python
General useful libraries
- BioPython
- bx-python
- NumPy/SciPy
- panda
- statsmodels
- beautiful soup
- matplotlib
- ipython
- PyCogent
- fuzzywuzzy
- pattern
- pysam
- ete2 - For phylogenetic trees
