REMAP marker for evaluating genetic diversity of cyprinus carpio population
A marker, carp technology, applied in the direction of DNA/RNA fragment, recombinant DNA technology, microbial determination/inspection, etc., can solve the problem of few fish research and so on
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[0018] 1. Acquisition of carp genome sequence
[0019] The carp genome was sequenced using a 454 high-throughput sequencer to obtain 0.01X coverage and a sequencing depth of 1.
[0020] 2. Identification process of carp LTR sequence
[0021] Identification of transposon taxa from fragment sequences in the carp genome:
[0022] Use the RepeatModeler (http: / / www.repeatmasker.org / RepeatModeler.html) of the Repeat masker software to perform denovo repeat sequence identification;
[0023] Identify sequences containing retrotransposons:
[0024] Use blastn to confirm the presence of transport-related proteins in TE: blastx alignment of these sequences with the amino acid sequences of zebrafish retrotransposons (http: / / www.repeatmasker.org / RepeatProteinMask.html#database). Sort all translocation-related encoded proteins by length;
[0025] Identification of full-length retrotransposon sequences:
[0026] Use the software LTR FINDER to scan candidate sequences, and select sequenc...
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