Download Shareware and Freeware Software for Windows, Linux, Macintosh, PDA

line Home  |  About Us  |  Link To Us  |  FAQ  |  Contact

Serving Software Downloads in 976 Categories, Downloaded 30.067.962 Times

Bio::Tools::Run::PiseApplication::consensus 1.4

  Date Added: January 07, 2010  |  Visits: 1.260

Bio::Tools::Run::PiseApplication::consensus

Report Broken Link
Printer Friendly Version


Product Homepage
Download (76 downloads)

Bio::Tools::Run::PiseApplication::consensus is a Perl module. Bioperl class for: CONSENSUS Identification of consensus patterns in unaligned DNA and protein sequences (Hertz, Stormo) References: G.Z. Hertz and G.D. Stormo. Identification of consensus patterns in unaligned DNA and protein sequences: a large-deviation statistical basis for penalizing gaps. In: Proceedings of the Third International Conference on Bioinformatics and Genome Research (H.A. Lim, and C.R. Cantor, editors). World Scientific Publishing Co., Ltd. Singapore, 1995. pages 201--216. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/consensus.html for available values): consensus (Excl) Program to run sequence (Sequence) Sequences file (-f) pipe: seqsfile width (Integer) Width of pattern (consensus only) (-L) out (String) consensus_matrix (String) complement (Excl) Complement of nucleic acid sequences (-c) ascii_alphabet (InFile) Alphabet and normalization information (if not DNA) (-a) prior (Switch) Use the designated prior probabilities of the letters to override the observed frequencies (-d) dna (Switch) Alphabet and normalization information for DNA protein (Switch) Alphabet and normalization information for protein queue (Integer) Maximum number of matrices to save between cycles of the program -- ie: queue size (-q) standard_deviation (Float) Number of standard deviations to lower the information content at each position before identifying information peaks (mandatory for wconsensus) (-s) progeny (Excl) Save the top progeny matrices (-pr1) linearly (Switch) Seed with the first sequence and proceed linearly through the list (-l) max_cycle_nb (Integer) Maximum repeat of the matrix building cycle (-n or -N) max_cycle (Excl) How many words per matrix for each sequence to contribute (-n or -N) distance (Integer) Minimum distance between the starting points of words within the same matrix pattern (-m) terminate (Integer) Terminate the program this number of cycles after the current most significant alignment is identified (-t) terminal_gap (Excl) Permit terminal gaps (-pg) (wconsensus only) top_matrices (Integer) Number of top matrices to print (-pt) final_matrices (Integer) Number of final matrices to print (-pf).

Requirements: No special requirements
Platforms: Linux
Keyword: Biotoolsrunpiseapplicationconsensus Consensus Dna Excl Information Integer Libraries Matrices Number Piseapplication Programming
Users rating: 0/10

License: Freeware Size: 829.44 KB
BIO::TOOLS::RUN::PISEAPPLICATION::CONSENSUS RELATED
Libraries  -  Bio::Tools::Run::PiseApplication::fasta 1.4
Bio::Tools::Run::PiseApplication::fasta is a Bioperl class for sequence database search. Parameters: fasta (Excl) Fasta program query (Sequence) Query sequence File pipe: seqfile seqtype (Excl) Is it a DNA or protein sequence (-n)...
82.94 KB  
Mathematics  -  Integer To Decimal 1.0
IntegerToDecimal allows you to enter an integer (base 10) number which it converts to any base between 2 and 16 inclusive. You may enter negative numbers as well. Currently the application supports 16 bit integers. Source code is also available on...
26 KB  
Audio Tools  -  Mp3dings 1.0 / 2.0 Beta 1
Mp3dings is a small, powerful and easy-to-use program that allows you to change the names and edit the meta-information of a large number of mp3 files at the same time..
1024 KB  
Mathematics  -  giantint 1.0
The giantint package consists of a library of routines for large integer arithmetic and number theory. PSI plans to augment this free software release in future, with other topical folders.
38 KB  
Utilities  -  EZNetInfo 1.2+
EZNetInfo is a tool which provides vital networking information with a minimum number of clicks. Want to know your current IP address? Simply hover your mouse over the icon in the system tray and it will output your IP address. Need to know more...
122 KB  
Specialized Tools  -  Softreg 2009 2.0.0.965
Softreg 2009 stores your Customers Information, Program Name, Serial Number, Price Paid, Date etc... It also lets you Sort, Search, Print Preview, Print, Export Data and More! The file includes Professional Install and un-Install features and a...
9.71 MB  
Information Lookup  -  Mobile Number Tracer 1.0
Mobile Number Tracer traces the information about any mobile number code like Service Provider, State, or Reference City. It is useful for tracing out from where a user got a missed call. Mobile Number Tracer is valid for India only. It also...
 
Database Tools  -  xDatabase 1.0
xDatabase is a simple MySQL database access wrapper.Functions of xDatabase:- xDatabase can connect to database from the class constructor.- xDatabase is possible to use a single function to execute queries and retrieve results.- xDatabase...
10 KB  
Business  -  PPL CZ 1.1.0.0
Shipping company PPL CZ s.r.o. brings new Windows Phone 8 application which enables users to check the current state of delivery package and much more useful information like: - delivery package number - shipper information -...
19 MB  
Reference  -  RLX Watch Guide 1.4.0.0
This little "pocket" guide for your Windows Phone 7 is a light guide to help and support you when exploring the world of Rolex Oyster Perpetual watches. ~~~ I tried to capture interesting and relevant information on a selected number of...
1024 KB  
NEW DOWNLOADS IN PROGRAMMING, LIBRARIES
Programming  -  FLEX-db Digital Asset Manager 3.0.9
FLEX-db - an enterprise Digital Asset Manager (DAM). It ingests and links metadata with files, creates thumbnails, and processes files using business rules. FLEX-db has a JSP client, Java app server for file input and output and an EJB metadata...
21.57 MB  
Programming  -  Libicom 0.9.0
The libicom library is a character based dynamicly linked library for Linux. It is used to remotely control the Icom IC-R8500 wide band receiver via an RS232 link. All call and return parameters to the control functions are character string based....
20.48 KB  
Programming  -  dotdesktop 0.3
Dotdesktop library provides ability to parse desktop entry file and access the information in a convenient way. Desktop entry file format is defined by freedesktop.org, it is used to describe information about an application such as the name and...
327.68 KB  
Programming  -  Cedalion for Linux 0.2.6
Cedalion is a programming language that allows its users to add new abstractions and define (and use) internal DSLs. Its innovation is in the fact that it uses projectional editing to allow the new abstractions to have no syntactic limitations.
471.04 KB  
Programming  -  libyasl 0.2
Libyasl is a C++ class library to easily realize TCP/UDP/Multicast clientsand servers in IPv4 and IPv6 environments under GNU/Linux systems.
143.36 KB  
Libraries  -  wolfSSL 3.12.0
The wolfSSL embedded SSL/TLS library is a lightweight SSL library written in ANSI standard C and targeted for embedded and RTOS environments - primarily because of its small size, speed, and feature set. It is commonly used in standard operating...
2.73 MB  
Libraries  -  EuGTK 4.8.9
Makes it easy to develop good- looking, fast, cross-platform programs that run on Linux, OS X, and Windows. Euphoria is a very fast interpreted/compiled language with straight-forward syntax. EuGTK allows programming in a clean, object-oriented...
10.68 MB  
Libraries  -  Linux User Group Library Manager 1.0
The LUG Library Manager is a project to help Linux User Groups start their own library. A LUG library is helpful to the community at large because it increases access to information, and gives everyone the opportunity to become more knowledgeable.
5.35 KB  
Libraries  -  Module::MakefilePL::Parse 0.12
Module::MakefilePL::Parse is a Perl module to parse required modules from Makefile.PL. SYNOPSIS use Module::MakefilePL::Parse; open $fh, Makefile.PL; $parser = Module::MakefilePL::Parse->new( join("", ) ); $info = $parser->required;...
8.19 KB  
Libraries  -  sqlpp 0.06
sqlpp Perl package is a SQL preprocessor. sqlpp is a conventional cpp-alike preprocessor taught to understand SQL ( PgSQL, in particular) syntax specificities. In addition to the standard #define/#ifdef/#else/#endif cohort, provides also...
10.24 KB