文件列表:

Example (0, 2020-04-16)
Example\DNA.fasta (22344, 2020-04-16)
Example\Protein.fasta (3426, 2020-04-16)
Model (0, 2020-04-16)
Model\Combine_Model.zip (14247593, 2020-04-16)
Model\Combine_Scale (45455, 2020-04-16)
Model\Embryogenesis_Model (19360484, 2020-04-16)
Model\Embryogenesis_Scale (45787, 2020-04-16)
Model\Oogenesis_Model (9993151, 2020-04-16)
Model\Oogenesis_Scale (46482, 2020-04-16)
Model\Spermatogenesis_Model (18775927, 2020-04-16)
Model\Spermatogenesis_Scale (45520, 2020-04-16)
PrESOgenesis (28864, 2020-04-16)
PrESOgenesis.c (84723, 2020-04-16)
Scripts (0, 2020-04-16)
Scripts\Features.R (783, 2020-04-16)
Scripts\TransDecoder-3.0.1 (0, 2020-04-16)
Scripts\TransDecoder-3.0.1\Changelog.txt (879, 2020-04-16)
Scripts\TransDecoder-3.0.1\LICENSE.txt (1492, 2020-04-16)
Scripts\TransDecoder-3.0.1\Makefile (197, 2020-04-16)
Scripts\TransDecoder-3.0.1\PerlLib (0, 2020-04-16)
Scripts\TransDecoder-3.0.1\PerlLib\Fasta_reader.pm (3479, 2020-04-16)
Scripts\TransDecoder-3.0.1\PerlLib\Fasta_retriever.pm (1564, 2020-04-16)
Scripts\TransDecoder-3.0.1\PerlLib\GFF3_utils.pm (8383, 2020-04-16)
Scripts\TransDecoder-3.0.1\PerlLib\Gene_obj.pm (142703, 2020-04-16)
Scripts\TransDecoder-3.0.1\PerlLib\Gene_obj_indexer.pm (1362, 2020-04-16)
Scripts\TransDecoder-3.0.1\PerlLib\Longest_orf.pm (11642, 2020-04-16)
Scripts\TransDecoder-3.0.1\PerlLib\Nuc_translator.pm (10298, 2020-04-16)
Scripts\TransDecoder-3.0.1\PerlLib\TiedHash.pm (3707, 2020-04-16)
Scripts\TransDecoder-3.0.1\TransDecoder.LongOrfs (10429, 2020-04-16)
Scripts\TransDecoder-3.0.1\TransDecoder.Predict (13134, 2020-04-16)
Scripts\TransDecoder-3.0.1\notes (120, 2020-04-16)
Scripts\TransDecoder-3.0.1\transdecoder_plugins (0, 2020-04-16)
Scripts\TransDecoder-3.0.1\transdecoder_plugins\Makefile (249, 2020-04-16)
Scripts\TransDecoder-3.0.1\transdecoder_plugins\cd-hit-v4.6.1-2012-08-27.tgz (652425, 2020-04-16)
... ...

# PrESOgenesis 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. $ gzip -dc PrESOgenesis.tar.gz | tar x $ cd PrESOgenesis $ chmod 777 /full/path/to/install.sh $ /full/path/to/install.sh 4) Run PrOSEgenesis $ /full/path/to/PrESOgenesis /full/path/to/Candidates.fa 5) Output The results will be stored in PrESOgenesis_resultss.txt. 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.

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