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mipe2dbsts(1) [debian man page]

MIPE2DBSTS(1)						User Contributed Perl Documentation					     MIPE2DBSTS(1)

NAME
mipe2dbSTS.pl - Generates input file for submission to dbSTS included in output: STS section of dbSTS submission based on MIPE version v1.1 arguments: * mipe_file * config file * (optional) list of PCR IDs The config file consists of lines containing a key and a value, separated by an equal sign ('='). The key consists of the lowercase name of the NCBI submission file (see website dbSTS), followed by an underscore and the lowercase name of the field in that file. The following fields should be defined in the config file: pub_title= pub_authors= source_name= source_organism= cont_name= cont_fax= cont_tel= cont_email= cont_lab= cont_inst= cont_addr= protocol_name= protocol_protocol= buffer_name= buffer_buffer= sts_pcr_profile= For protocol_protocol, buffer_buffer and sts_pcr_profile, more lines are necessary (see example). An example of a config file look like this: pub_title=Genetic mapping of chicken SNPs pub_authors=Aerts,J.A.; Veenendaal,T.; Crooijmans,R.P.M.A; Groenen,M.A.M source_name=Chicken genomic DNA source_organism=Gallus gallus cont_name=Jan Aerts cont_fax=+31 317 483929 cont_tel=+31 317 483397 cont_email=jan.aerts@wur.nl cont_lab=Animal Breeding and Genomics Group cont_inst=Wageningen University cont_addr=PO Box 338, 6700 AH Wageningen, The Netherlands protocol_name=Protocol_Aerts protocol_protocol=Template: 30-60 ng protocol_protocol=Primer: each 4 uM protocol_protocol=dNTPs: each 200 uM protocol_protocol=Taq: 0.3 units protocol_protocol=Volume: 12 ul buffer_name=Buffer_Aerts buffer_buffer=MgCl2: 1.5 mM buffer_buffer=(NH4)2SO4: 20 mM buffer_buffer=Tris-HCl: 75 mM buffer_buffer=Tween 20: 0.01% (w/v) buffer_buffer=pH: 8.8 BUGS
Unknown. If you encounter one, please let me know (jan.aerts@wur.nl). SYNOPSIS
mipe2dbSTS.pl your_file.mipe dbSTS.config <pcr_id1> <pcr_id2> ADDITIONAL INFO
See http://mipe.sourceforge.net AUTHOR
Jan Aerts (jan.aerts@bbsrc.ac.uk) perl v5.14.2 2005-07-20 MIPE2DBSTS(1)

Check Out this Related Man Page

PERLPRIMER(1)						      General Commands Manual						     PERLPRIMER(1)

NAME
perlprimer - graphically specify amplicon of DNA or mRNA sequences and design primers SYNOPSIS
perlprimer DESCRIPTION
PerlPrimer calculates primer melting temperature using J. SantaLucia's extensive nearest-neighbour thermodynamic parameters. To adjust for the salt conditions of the PCR, PerlPrimer uses the empirical formula derived by von Ahsen, et al. (2001) and allows the user to specify the concentration of Mg2+, dNTPs and primers, or use standard PCR conditions. The result is a highly accurate prediction of primer melting temperature, giving rise to a maximum yeild of product when amplified. PerlPrimer is written in Perl and requires Perl/Tk. In addition, for QPCR functionality PerlPrimer requires the open-source Spidey executable from NCBI. The program is designed to be cross-platform com- patible and has been developed and tested on both Microsoft Windows and GNU/Linux-based operating systems. Users have also reported success using the program under Mac OS X. SEE ALSO
A very nice tutorial on http://perlprimer.sourceforge.net is also distributed as a debian package perlprimer-doc. AUTHOR
perlprimer was written by Owen Marshall <owenjm@users.sourceforge.net> This manual page was assembled by Steffen Moeller <steffen_moeller@gmx.de>, for the Debian project (but may be used by others). 6 January 2005 PERLPRIMER(1)
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