https://github.com/pseudogene/uniprime

A workflow-based platform for improved Universal Primer design
https://github.com/pseudogene/uniprime

bioinformatics genbank pcr primer taxonomy universal-primers

Last synced: about 2 months ago
JSON representation

A workflow-based platform for improved Universal Primer design

• Host: GitHub
• URL: https://github.com/pseudogene/uniprime
• Owner: pseudogene
• License: other
• Created: 2015-12-07T15:04:23.000Z (about 9 years ago)
• Default Branch: master
• Last Pushed: 2015-12-08T11:20:22.000Z (about 9 years ago)
• Last Synced: 2024-07-30T19:59:37.280Z (6 months ago)
• Topics: bioinformatics, genbank, pcr, primer, taxonomy, universal-primers
• Language: PHP
• Homepage:
• Size: 183 KB
• Stars: 1
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README
  • License: LICENSE

Awesome Lists containing this project

README

        
# $Id: README,v 2.10 2012/09/07 12:35:58 Scotland/Stirling $

                          UniPrime (Ootoowerg) README

o INSTALLATION

o TUTORIAL

o COMMAND REFERENCE

o FAQ

o INSTALLATION

  See the INSTALL file.

o TUTORIAL

 Here is a simple example of a full execution of UniPrime. Each step can be

 reviewed with the web-companion interface.

 The files you will need uniprime.pm and UniTools.pm are in directory 'bin'

 of the distribution package.

   1. Add a new locus and use the human OAZ1 gene as prototype. The GeneID

   (4946) is retrieved from GenBank (from the command line in a Terminal

   window):

     ./uniprime.pl --action=locus --target=4946 -v

   2. Use the locusID provided (e.g. L3.1) and look for orthologues within

   the class Mammalia and an e-value of 2e-50 as threshold:

     ./uniprime.pl --action=ortho --target=L3.1 -e=2e-50 --query=Mammalia[ORGN] -v

   3. Use the locusID (e.g. L3.1) and establish an alignment and a consensus

   sequence with a threshold of 60%:

     ./uniprime.pl --action=align --target=L3.1 -c=60 -v

   4. Use the AlignmentID (e.g. A3.2) and design the primer sets:

     ./uniprime.pl --action=primer --target=A3.2 -v

   5. Optionally, use the primer set (e.g. X3.3) and do a virtual PCR with the

   Mammalian sequence of the WGS databank of the NCBI.

     ./uniprime.pl --action=vpcr --target=X3.3 --db=wgs --query=Mammalia[ORGN] -v

o COMMAND REFERENCE

 There is only one file controlling UniPrime in bin/uniprime.pl.

 You may find more help by using the command-line help of this file.

     ./uniprime.pl --help

 There are five main functions: adding a new locus/gene; searching

 for the orthologous sequences in other species; establishing the

 alignment; designing the primer set and doing a virtual PCR if

 necessary:

     uniprime.pl --action= --target= [options]

  Available actions are:

   'locus'   Add a new locus:

    --target GenBank GeneID to be used for this action or fasta file to be used.

             (mandatory*)

    --pmid   Associate a reference. (PMID)

   'ortho'   Find new orthologues from mRNA sequences of the locus prototype

             with BLASTN with the following options:

    --target LocusID to be used for this action. (mandatory*)

    --db     Database used when performing the tblastx search. (default

             value 'refseq_rna')

    --query  the BLAST search can be limited to the result of an Entrez query

             against the database chosen. (default none; e.g. 'viruses[ORGN]')

    --dna    Use DNA rather than mRNA as initial input sequence. (default mRNA)

    -e       Set the E-value threshold. It is a positive real number. The

             default is 1e-100. Hit with E-value better than (less than)

             this threshold will be shown.

   'align'   Provide alignment using T-coffee:

    --target LocusID to be used for this action. (mandatory*)

    --dna    Use DNA rather than mRNA as initial input sequence. (default mRNA)

    -c       Set the threshold to establish the consensus sequence. It is a

             positive number between 0 and 100. (default 60)

    --select Specify the sub-set of sequence used for the alignement. (e.g.

             --select=S3.1 --select=S3.2 --select=S3.4 specify 3 sequences

             only S3.1, S3.2 and S3.4)

   'primer'  Identify universal primers from consensus sequence:

    --target AlignmentID to be used for this action. (mandatory*)

    --size   Optimal size of the amplification. (default 600)

   'vPCR'    Virtual-PCR retrieving all amplicons:

    --target 'PrimerID to be used for this action. (mandatory*)

    --db     Database used when performing the tblastx search. (default

             value 'wgs')

    --query  the BLAST search can be limited to the result of an Entrez query

             against the database chosen. (default 'viruses[ORGN]')

   Global options:

    --aligner either GramAlign or T-coffee. (Default GramAlign)

    -v       Print verbose output.

o FAQ

 Q: Where can I found more help?

 A: UniPrime home page is now https://code.google.com/p/uniprime/