_____ _ _ _____ _
/ ____(_) | / ____| | |
| (___ _| |_ ___| (___ ___| |_
\___ \| | __/ _ \\___ \ / _ \ __|
____) | | || __/____) | __/ |_
|_____/|_|\__\___|_____/ \___|\__|
_ _ _ _ _
| | | | | | (_) | |
| |_ ___ ___ | | | | __ _ | |_
| __| / _ \ / _ \ | | | |/ / | | | __|
| |_ | (_) | | (_) | | | | < | | | |_
\__| \___/ \___/ |_| |_|\_\ |_| \__|
=== SiteSet toolkit v0.1 =========
==================================
Toolkit for rapid analysis functional sites in nucleotide sequences.
For install all requirements run in work directory:
pip install -r requirements.txt
=== Toolkit structure: ===========
==================================
=== SemiSite (BSite) ===
========================
Localizing of semi-specific binding sites (bs) of RNA-binding proteins (RBP)
using local alignment algorithm.
W Weak
S Strong
M aMino
K Keto
R puRine
Y pYrimidine
B not A (B comes after A)
D not C (D comes after C)
H not G (H comes after G)
V not T (V comes after T and U)
N any Nucleotide (not a gap)
Z Zero
=== LacPars ============
========================
Parsing localization of elected binding sites.
=== SSite ==============
========================
Splice sites (ss) extractions orient by exon features location,
score calculating by MaxEnt algorithm and output CSV dataframe generating
(Yeo G and Burge C.B., Maximum Entropy Modeling of Short Sequence Motifs with
Applications to RNA Splicing Signals, Journal of Computational Biology,
in press; Copyright 2004, Gene Yeo, Chris Burge).
=== Config file structure ========
==================================
File with extension ".config" are require for setting up list of RBP
and them bindings sites in extension nucleotide notation.
Default config file name for SemiSite (BSite)
and LocPars tools are "factors.config".
Data presentation format:
YTHDC1,GGACH
SRSF3,CHWCHMC
SRSF10,TVAAGAHY
"factor_dep.config":
YTHDC1,False
SRSF3,True
SRSF10,True
=== Log file structure ===========
==================================
That's all!