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MirrorTree_v2.0_Beta

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Elba Raimúndez edited this page Mar 16, 2015 · 3 revisions

MIRRORTREE 2.0 - Beta

This is the PYT and SBI project developed by Elba Raimúndez, Clàudia Fontserè and Lucas Michel.

##What is new in mirrorTree 2.0 mirrorTree 2.0 is a program to predict protein-protein interactions using similarity between two protein families (Pazos and Valencia, 2001).

It can be initiated from two protein sequences in the same fasta file (with .fa/.fasta extension) or two multiple sequence alignments (two files with .aln extension, containing the query sequences).

The workflow of mirrorTree is the following:

  • Input a fasta file with two proteins (fasta format).
  • Find orthologs from each protein. This is done by connecting to BLAST (online) and comparing to swissprot/uniprot database.
    • The parameters controlling the BLAST search are % identity (according with the BLAST alignment) and e-value. By default these parameters are set to ≥30% and ≤1e-5 and ≥60% respectively, and they can be modified by the user.
    • Retain sequences that belong to the same species in both families. And only 1 sequence per organism, the one with highest homology with the query is chosen.
  • The resulting sequences are aligned using ClustalW (Thompson JD, 1994) with default parameters. This step is performed locally. As a result of this process, we obtain a multiple sequence alignment of the orthologs for our two query sequences.
  • (The user may start the execution here)
  • Afterwards, distance matrices for both alignments are computed. Phylogenetic trees are obtained from these alignments with the neighbor-joining (NJ) algorithm implemented in ClustalW (Chenna, et al., 2003) using bootstrap (100 repetitions).
  • Finally, The tree similarity between the two families is calculated as the correlation between their distance matrices using Pearson correaltion (Pazos and Valencia, 2001)

As a new feature, a graphical interface has been developed for mirrorTree 2.0, which will be more interactive for the user and easier to work with (for those who do not get along with the command line). This is still a beta version which is not working properly yet. It only allows to load the files, we are improving to get it to work as soon as possible!

##Requirements before installing

  • Beware that this script is written in Python 3.4.2. Check your version before executing mirrorTree.
  • Required python modules
  • ClustalW locally installed is required to run this script. Remember to change the clustalw path to your local path in modules.py.
  • Internet connection is needed to perform BLAST.

##Installation

The instructions for the proper installation of mirrorTree 2.0 are the following:

  • Remember! Make sure your ClustalW path is modified in modules.py.
  • Root privileges are needed for installation.
  • The following commands should be called in the command line inside the directory /install/:

sudo python3 setup.py install

##Organization of the code mirrorTree 2.0 package contains:

This program is split in different modules and scripts. Here, you can find the reference of what is contained in each file.

#####mirrorTree The main scripts are found in this directory.

  • __init__.py: A python file required for a proper installation of the program.
  • mirrorTree_beta: The workflow of the program. In this script all functions needed are called. It also contains the argument parser.
  • functions.py: All the core, helper functions and classes are found here. The documentation of each function is available in this file.
  • modules.py: In this files you can find the ClustalW path and all modules that the program needs to run. From this file they are imported to the others.
  • visual.py: In this program we have the graphical interface for mirrorTree 2.0!

#####setup.py The script needed to install the package.

##How to execute mirrorTree 2.0

This script is executed in the command line as following:

If starting from the two protein sequences (fasta format with extension .fa/.fasta): mirrorTree_beta -i input.fa

If starting from the two alignments (clustalW alignment with extension .aln): mirrorTree_beta -i input1.aln input2.aln

If starting from the graphical interface:

mirrorTree_beta -vi

There are other parameter:

  • -v: verbose. To see more detailed stderr.
  • -s: save. To save tmp files.
  • -o: output. To save data into a predefined output file. By default they are shown as stdout.
  • -e: evalue. Change threshold of Blast filtering. By default it is set in 0.00001.
  • -id: identity. Change threshold of Blast filtering. By default it is set in 30.

If any doubt:

mirrorTree_beta -h

This will show you how to execute the script.

2015 - Elba Raimúndez, Clàudia Fontserè and Lucas Michel

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