.\" Automatically generated by Pod::Man 4.14 (Pod::Simple 3.40) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. 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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "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 .PP .Vb 10 \& The config file consists of lines containing a key and a value, separated by an equal sign (\*(Aq=\*(Aq). \& 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 .Ve .SH "BUGS" .IX Header "BUGS" Unknown. If you encounter one, please let me know (jan.aerts@wur.nl). .SH "SYNOPSIS" .IX Header "SYNOPSIS" mipe2dbSTS.pl your_file.mipe dbSTS.config .SH "ADDITIONAL INFO" .IX Header "ADDITIONAL INFO" See http://mipe.sourceforge.net .SH "AUTHOR" .IX Header "AUTHOR" Jan Aerts (jan.aerts@bbsrc.ac.uk)