mipe08to09(1) [debian man page]

MIPE08TO09(1)						User Contributed Perl Documentation					     MIPE08TO09(1)

NAME

       mipe08to09 - Reads a MIPE file version 0.8 and prints it in version 0.9

SYNOPSIS

       mipe08to09 yourfile-in-version-0.8.mipe

ADDITIONAL INFO

       See http://mipe.sourceforge.net

AUTHOR

       Jan Aerts (jan.aerts@bbsrc.ac.uk)

perl v5.14.2							    2012-02-18							     MIPE08TO09(1)

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)