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ReadMe.txt
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===============================================================================================
= ============ === ===== =================================================
= ==== =========== ======== ==== === == ================================================
= ==== =========== ======== ==== == ==== ===============================================
= ==== == = === ========= ======= ==== === ==== === = ==== ==== === === ==
= === = == ======= ===== ==== == = == = == == = == = ====== = =
= ======== ======= ============= === ==== === == == = == === ==== === ===
= ======== ======= ======== ==== == ==== ===== == ===== = == ======= === ==== ==
= ======== ======= ======== ==== === == === = == = == = == = == = == == = =
= ======== ======= === ===== ===== ==== === = === ==== === === ==
===============================================================================================
= =
= Fertility Protein Predictor by: =
= =
= Mohammad Reza Bakhtiarizadeh =
= Maryam Rahimi =
= =
= =
= University of Tehran${bold} =
= =
= Contact: mrbakhtiari@ut.ac.ir =
= =
= Usage: /path/to/PrESOgenesis options /path/to/sequences.fasta =
= =
===============================================================================================
1) Introduction
PrESOgenesis is a Support Vector Machine-based classifier to predict the
spermatogenesis/embryogenesis/oogenesis related proteins based on 1920
meaningful protein sequence features. It takes protein/DNA FASTA sequences
as input, and generate output about the potential of a protein to be
involved in spermatogenesis/embryogenesis/oogenesis. PrESOgenesis depends
on two programs (libsvm and protr package in R) and can be run on Linux.
Also, it use TransDecoder software to convert the DNA sequences (mRNA
transcripts that converted to DNA) to protein.
2) Pre-requisite
It just need R software to be installed in your system.
3) Install dependencies
Drag install.sh file to terminal for automatic installing all of the
dependencies. This will build and install the libsvm and TransDecoder
software and protr package.
$ git clone https://github.com/mrb20045/PrESOgenesi
$ cd PrESOgenesis/
$ chmod 777 /full/path/to/install.sh
$ /full/path/to/install.sh
4) Run PrESOgenesis
$ /full/path/to/PrESOgenesis /full/path/to/Candidates.fa
5) Output
The results will be stored in PrESOgenesis_resultss.txt. An example of PrESOgenesis
output is presented here. The score represents a protein's probability of belonging
to the spermatogenesis/embryogenesis/oogenesis. PrESOgenesis applied a probability
score >0.5 to designate putative related protein.
############################
# PrESOgenesis Results #
# #
# 19/08/2017 16:16:03 #
############################
Total number of processed sequences: 7
______________________________________________________________________________________________________________________________________________________
Protein_ID Fertility (Score) Type Embryogenesis_Score Oogenesis_Score Spermatogenesis_Score
______________________________________________________________________________________________________________________________________________________
tr|E3M642|E3M642_CAERE No (0.26) _ _ _ _
______________________________________________________________________________________________________________________________________________________
tr|H2VGR2|H2VGR2_CAEJA No (0.42) _ _ _ _
______________________________________________________________________________________________________________________________________________________
tr|B4R5E9|B4R5E9_DROSI Yes (0.65) Oogenesis 0.68 0.94 0.72
______________________________________________________________________________________________________________________________________________________
tr|G2J611|G2J611_DROME Yes (0.69) Oogenesis 0.76 0.99 0.74
______________________________________________________________________________________________________________________________________________________
tr|A0A0J9S1Y5|A0A0J9S1Y5_DROSI Yes (0.80) Oogenesis 0.73 0.94 0.36
______________________________________________________________________________________________________________________________________________________
tr|A0A0M5JA66|A0A0M5JA66_DROBS Yes (0.85) Oogenesis 0.77 0.94 0.43
______________________________________________________________________________________________________________________________________________________
tr|A0A0M4EYE9|A0A0M4EYE9_DROBS No (0.38) _ _ _ _
______________________________________________________________________________________________________________________________________________________
Summary of the Resuts
_____________________________________________________________
Title Score>0.5 Score>0.75 Score>0.90
_____________________________________________________________
Fertiliy 4 2 0
Embryogenesis 4 2 0
Oogenesis 4 4 4
Spermatogenesis 2 0 0
_____________________________________________________________