资 源 简 介
Our system implementation consists of the following steps:
Predict microsatellites with Tandem Repeats Finder (TRF) using the following the command trf 2 7 7 80 10 25 500 -d -h where is path to a FASTA file containing nucleotide sequences.
Deposit all the raw reads, reference genomes and predicted microsatellite to the PostgreSQL database.
Assign SSRs to canonical consensuses.
Demultiplex samples if necessary, hidden Markov model (HMM) topology that we use to demultiplex reads with universal amplification primers.
Use crude clustering procedure, first subdividing reads based on canonical consensus assigned to detected SSRs. Groups of SSRs sharing the same canonical consensus and a number of oligonucleotides (7 bp long) above certain threshold on both flanks are called crude clusters. All the predicted crude clusters are stored in the database.
Use MUSCLE program to distill loci from
