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mipe2dbSTS

Langue: en

Version: 2005-07-20 (debian - 07/07/09)

Section: 1 (Commandes utilisateur)

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)
CHASSE, PÊCHE, NATURE ET TRADITION

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