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MIPE2DBSTS

MIPE2DBSTS

Section: User Contributed Perl Documentation (1) Updated: 2005-07-20
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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)


 

Index

NAME
BUGS
SYNOPSIS
ADDITIONAL INFO
AUTHOR

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Time: 21:23:54 GMT, April 16, 2011