FONZIE Find markers with with this tool
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marker cartography genetics

FONZIE Description

FONZIE is a Python-based informatics application that was created for the genetic cartography speciality. FONZIE allows you to find markers on a set of sequences and associate oligonucleotides as well. FONZIE calls Tandem Repeat Finder on the input nucleic sequence file (FASTA format). Each marker is screened regarding different criteria (size, percent of matches, presence in specific regions of the input sequence). Then, marker's sensitivity is established by performing a BLAST against a database of nucleic sequences (which include the input file). This database has to be created before the use of FONZIE. In the next step, primer pairs are designed, using Primer3, for the selected markers. FONZIE then test the sensitivity of the amplification product using BLAST against the database. The output files of FONZIE are a tab-delimited text file including data on markers and primers, a dat file which is the output of TRF and 3 directories containing respectively, the marker sequence in FASTA, the amplification product sequence in FASTA and a data file for each marker.

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