Remerciez-le!

Remerciez @Admin pour avoir partagé cet document gratuitement, de la manière la plus simple, en partageant sur les réseaux sociaux.

User guide 18 User Guide for propy What is this This document is intended to provide an overview of how one can use the propy functionality from Python It ? s not comprehensive and it ? s not a manual If you ?nd mistakes or have suggestions for improvemen

User Guide for propy What is this This document is intended to provide an overview of how one can use the propy functionality from Python It ? s not comprehensive and it ? s not a manual If you ?nd mistakes or have suggestions for improvements please either ?x them yourselves in the source document the py ?le or send them to the mailing list orietal- cds hotmail com Install the propy package propy has been successfully tested on Linux and Windows systems The author could download the propy package from http code google com p protpy downloads list zip and tar gz The install process of propy is very easy On Windows download the propy package zip extract or uncompress the zip ?le cd propy- python setup py install On Linux download the propy package tar gz tar -zxf propy- tar gz cd propy- python setup py install or sudo python setup py install Download proteins from Uniprot CYou can get a protein sequence from the Uniprot website by providing a Uniprot ID You can get the window ? sub-sequences whose central point is the given amino acid ToAA You can also get several protein sequences by providing a ?le containing Uniprot IDs of these proteins CThe downloaded protein sequences have been saved in F target txt You could check whether the input sequence is a valid protein sequence or not The output is the number of the protein sequence if it is valid otherwise Obtaining the property from the AAindex database You could get the properties of amino acids from the AAindex database by providing a property name e g KRIW The output is given in the form of dictionary If the user provides the directory containing the AAindex database the AAindex database could be downloaded from ftp ftp genome jp pub db community aaindex It consists of three ?les aaindex aaindex and aaindex the program will read the given database to get the property CIt should be noted that the propy package has contained the AAindex database The GetAAIndex methods in AAIndex will get the property from the aaindex database If the user does not provide the directory containing the AAindex database the program will downlaod the three databases i e aaindex aaindex and aaindex to obtain the property It should be noted that the downloaded AAindex will be saved in the current directory You can also specify the directory according to your needs The downloaded databases are saved in F disk The GetAAIndex methods in AAIndex will get the property from the aaindex and aaindex databases Calculating protein descriptors There are two ways to calculate protein descriptors in the propy package One is to directly use the corresponding methods the other one is ?rstly to construct a GetProDes class and then run their methods to obtain the protein descriptors It should be noted that the output is a dictionary form whose keys and values represent the descriptor name and the descriptor value respectively The user could