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programs and scripts, mainly python, for analyses related to nucleic or protein sequences
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AdjustFASTA_or_FASTQ
Adjust_Annotation
Adjust_lists
CompareFASTA_or_FASTQ
ConvertSeq
Extract_Conserved_from_Aligned
Extract_Details_or_Annotation
Extract_from_FASTA
FindSequence
LookUpTaxon
RetrieveSeq
SOLiD
alignment-utilities
blast-utilities
circos-utilities
count_triplets
ena-utilities
mcscan-utilities
patmatch-utilities
plot_expression_across_chromosomes
plot_read_data
plot_sites
README.md

README.md

sequencework

Mainly python scripts related to nucleic or protein sequence work

I sorely need to put an index here with links to better guide to the appropriate folders. <== TO DO
(For now look at the title of the folders to try and discern if it is something of interest.)

Descriptions of the scripts are found within README.md files in the sub folders.

Related 'Binderized' Utilities

Collection of links to launchable Jupyter environments where various sequence analysis tools work WITHOUT ANY NEED FOR ADDITIONAL EFFORT/INSTALLS. Many of my recent scripts are built with use in these environments in mind:

(Many of these include/feature Biopython, too, such as but I haven't made a one all encompassing one yet for that since I use it a lot as an underlying library.)

  • patmatch-binder - launchable Jupyter sessions for running command line-based PatMatch in Jupyter environment provided via Binder (Perl and Python-based).

  • blast-binder - launchable Jupyter sessions for running command line-based BLAST+ in Jupyter environment provided via Binder.

  • InterMine-binder - Intermine Web Services available in a Jupyter environment running via the Binder service. (See the guide to getting started with using Intermine sites and Jupyter using MyBinder-served Jupyter notebooks.)

  • mcscan-binder - MCscan software available in a launchable Jupyter environment running via the Binder service (Python 2-based), with an example workflow and some other use examples.

  • mcscan-blast-binder - MCscan and BLAST+ command line software available in a launchable Jupyter environment running via the Binder service (Python 2-based).

  • synchro-binder - SynChro software available in a launchable Jupyter environment running via the Binder service with Quick start and some other illustrations of its use.

  • cl_sq_demo-binder - launchable, working Jupyter-based environment that has a collection of demonstrations of useful resources on command line (or useable in Jupyter sessions) for manipulating sequence files. (Note: THIS WAS STARTED AFTER SEVERAL OTHER DEMO NOTEBOOKS (many meant to be static) MADE FOR SEQUENCE SCRIPTs, and hopefully slowly those will be added to here as well to be available in active form.)

  • clausen_ribonucleotides binder - Analyze ribonucleotide incorporation data from Clausen et al. 2015 data using script plot_5prime_end_from_bedgraph.py.

  • circos-binder - Circos software available in a launchable Jupyter environment running via the Binder service with tutorials illustrating use (TBD)(Perl and Python-based).

See also

My simulated data repo has some useful scripts and resources for generating simulated (mock / fake) sequence data, gene expression data, or gene lists.

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