Commit 66dd47fc by Eric Coissac

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parent 444e7179
......@@ -158,7 +158,7 @@ Examples
maximum amplified sequence lengths (excluding primers) are 50 bp and 500 bp, respectively. The
primers used are TCACAGACCTGTTATTGC and TYTGTCTGSTTRATTSCG (possibility to use
:doc:`IUPAC codes <../iupac>`). They amplify a short portion of the nuclear 18S gene. The
results are saved in the ``mysequence.ecopcr`` file.
results are saved in the *mysequence.ecopcr* file.
......@@ -168,14 +168,14 @@ Examples
> ecoPCR -d mydatabase -e 2 -l 80 -L 120 -D 50 -r 7742 \
TTAGATACCCCACTATG#C# TAGAACAGGCTCCTCTA#G# > mysequences.ecopcr
Launches an *in silico* PCR on mydatabase (see :doc:`obiconvert <./obiconvert>` for a description
of the database format), with a maximum of two mismatches for each primer, but with a perfect match
on the last two nucleotides of the 3' end of each primer (a perfect match can be enforced by adding
on the last two nucleotides of the 3' end of each primer (a perfect match can be enforced by adding
a '#' after the considered nucleotide). The minimum and maximum amplified sequence lengths (excluding
primers) are 80 bp and 120 bp, respectively. The ``-D`` option keeps 50 nucleotides on each side of
the *in silico* amplified sequences, (including the amplified DNA fragment plus the two target
sequences of the primers). The primers used are TTAGATACCCCACTATGC and TAGAACAGGCTCCTCTAG. They
sequences of the primers). The primers used are TTAGATACCCCACTATGC and TAGAACAGGCTCCTCTAG. They
amplify a short portion of the mitochondrial 12S gene. The ``-r`` option restricts the search to
vertebrates (7742 is the :doc:`taxid <../attributes/taxid>` of vertebrates). The results are saved
in the ``mysequence.ecopcr`` file.
......
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