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 32.290.235 Times

Bio::Restriction::Enzyme 1.4

  Date Added: August 26, 2010  |  Visits: 1.105


Report Broken Link
Printer Friendly Version

Product Homepage
Download (111 downloads)

Bio::Restriction::Enzyme is a single restriction endonuclease (cuts DNA at specific locations). SYNOPSIS # set up a single restriction enzyme. This contains lots of # information about the enzyme that is generally parsed from a # rebase file and can then be read back use Bio::Restriction::Enzyme; # define a new enzyme with the cut sequence my $re=new Bio::Restriction::Enzyme (-enzyme=>EcoRI, -seq=>G^AATTC); # once the sequence has been defined a bunch of stuff is calculated # for you: #### PRECALCULATED # find where the enzyme cuts after ... my $ca=$re->cut; # ... and where it cuts on the opposite strand my $oca = $re->complementary_cut; # get the cut sequence string back. # Note that site will return the sequence with a caret my $with_caret=$re->site; #returns G^AATTC; # but it is also a Bio::PrimarySeq object .... my $without_caret=$re->seq; # returns GAATTC; # ... and so does string $without_caret=$re->string; #returns GAATTC; # what is the reverse complement of the cut site my $rc=$re->revcom; # returns GAATTC; # now the recognition length. There are two types: # recognition_length() is the length of the sequence # cutter() estimate of cut frequency my $recog_length = $re->recognition_length; # returns 6 # also returns 6 in this case but would return # 4 for GANNTC and 5 for RGATCY (BstX2I)! $recog_length=$re->cutter; # is the sequence a palindrome - the same forwards and backwards my $pal= $re->palindromic; # this is a boolean # is the sequence blunt (i.e. no overhang - the forward and reverse # cuts are the same) print "bluntn" if $re->overhang eq blunt; # Overhang can have three values: "5", "3", "blunt", and undef # Direction is very important if you use Klenow! my $oh=$re->overhang; # what is the overhang sequence my $ohseq=$re->overhang_seq; # will return AATT; # is the sequence ambiguous - does it contain non-GATC bases? my $ambig=$re->is_ambiguous; # this is boolean print "Stuff about the enzymenCuts after: $can", "Complementary cut: $ocanSite:nt$with_caret orn", "t$without_caretn"; print "Reverse of the sequence: $rcnRecognition length: $recog_lengthn", "Is it palindromic? $paln"; print "The overhang is $oh with sequence $ohseqn", "And is it ambiguous? $ambignn"; ### THINGS YOU CAN SET, and get from rich REBASE file # get or set the isoschizomers (enzymes that recognize the same # site) $re->isoschizomers(PvuII, SmaI); # not really true :) print "Isoschizomers are ", join " ", $re->isoschizomers, "n"; # get or set the methylation sites $re->methylation_sites(2); # not really true :) print "Methylated at ", join " ", keys %{$re->methylation_sites},"n"; #Get or set the source microbe $re->microbe(E. coli); print "It came from ", $re->microbe, "n"; # get or set the person who isolated it $re->source("Rob"); # not really true :) print $re->source, " sent it to usn"; # get or set whether it is commercially available and the company # that it can be bought at $re->vendors(NEB); # my favorite print "Is it commercially available :"; print $re->vendors ? "Yes" : "No"; print " and it can be got from ", join " ", $re->vendors, "n"; # get or set a reference for this $re->reference(Edwards et al. J. Bacteriology); print "It was not published in ", $re->reference, "n"; # get or set the enzyme name $re->name(BamHI); print "The name of EcoRI is not really ", $re->name, "n"; This module defines a single restriction endonuclease. You can use it to make custom restriction enzymes, and it is used by Bio::Restriction::IO to define enzymes in the New England Biolabs REBASE collection. Use Bio::Restriction::Analysis to figure out which enzymes are available and where they cut your sequence..

Requirements: No special requirements
Platforms: Linux
Keyword: Biorestrictionenzyme Cut Cuts Dna Gaattc Libraries Not Really Print Programming Re- Restriction Restriction Endonuclease Sequence
Users rating: 0/10

License: Freeware Size: 4.7 MB
Audio Tools  -  aKode 2.0.2
aKode is not really a KDE application and not even an application, but very usefull non the less. aKode is the decoding library used in akode_artsplugin in kdemultimedia, and improves the aRts experience by fewer drop-outs, more supported...
460.8 KB  
Application Add-Ins  -  7-PDFMyURL 1.0
It is rare for PDF printers to allow you to create a PDF from a website without pages being -cut off- or the PDF not being -in one piece-; 7-PDFMyURL freeware now provides the solution! This special PDF Tool convert a website layouts cleany and in...
1.55 MB  
Finance  -  7-PDF Website Converter 1.0.2 Build 124
It is rare for PDF printers to allow you to create a PDF from a website without pages being -cut off- or the PDF not being -in one piece-; 7-PDF Website Cconverter now provides the solution! This special PDF Tool convert a website layouts cleany...
Utilities  -  Opti Contact 1.1
Is it contact sharing using Bluetooth, E-Mail or MMS not really convenient for you? Now you can share your contacts as vCards encoded in QR Barcodes. Opti Contact app will create these barcodes and iPhone companion will scan and import them. *...
1024 KB  
Modules  -  Login Menu 6.x-1.x-dev/5.x-1.x-dev 1.0
This is not really necessary in Drupal 6 as this functionality is also included in the core.InstallationUnpack in your modules folder (usually /sites/all/modules/) and enable under Administer > Site Building > Modules. Requirements: - Drupal 5.x/6.x
Modules  -  Firefox Search Plugin for OSC shops 1.0
This plugin is a Mozilla Firefox one, not really an oscommerce contribution. With this your customers will be able to add your site to the search engine box included in Firefox.This is specific to Firefox, it doesn't work with IE...
Modules  -  WP-TopScoredCommentAuthors 0.1
This plugin is a replacement for the default "Top Ten Comments" because that plugin did not really do what I wanted. In the default plugin shows ten people who gave the most comments ever. But if an author left 500 comments two years ago and left...
20.48 KB  
Development Editors  -  OSTicket Plus 11-23-2010
This is not really a fork of osticket just a space that i create to work with osticket internacionalization and maybe in future deploy with deb system
665.6 KB  
Entertainment  -  3StoogesReviewer 1
This app is totally useless- unpurpose- much like the movies the 3 stooges make. I am not really a fan so I'm being a bit harsh in these reviews, but you can't say I didn't warn you. I review over 20 of their "films". It's not much considering...
7.4 MB  
Utilities  -  GripType 1.2
Type while skydiving! Not really, but this top positioned keyboard makes typing with one hand safer and easier as you hold the device more firmly. The handgrip also makes it more difficult for thieves to snatch the device from your hand. It's also...
512 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  -  Math::GMPf 0.29
Math::GMPf - perl interface to the GMP library's floating point (mpf) functions.
30.72 KB  
Programming  -  Net::Wire10 1.08
Net::Wire10 is a Pure Perl connector that talks to Sphinx, MySQL and Drizzle servers. Net::Wire10 implements the low-level network protocol, alias the MySQL wire protocol version 10, necessary for talking to one of the aforementioned...
30.72 KB  
Programming  -  logilab-common 0.56.2
a bunch of modules providing low level functionnalities shared among some python projects devel Please note that some of the modules have some extra dependencies. For instance, logilab.common.db will require a db-api 2.0 compliant...
174.08 KB  
Programming  -  OpenSSL for linux 1.0.0a
The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolkit implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a...
3.83 MB  
Libraries  -  wolfSSL 3.15.3
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...
3.88 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