This is the command mipe2dbSTS that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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=[email protected]
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
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