SSR analysis of Blueberry 454 Unigene assembly

Analysis NameSSR analysis of Blueberry 454 Unigene assembly
MethodGDR SSR server and BLAST (NA)
Source454 Unigene Assembly from LJ Rowland
Date performed2011-02-03

This page describes the analysis that was carried out and has links to the raw data files.  For the final published results, please see the link to the paper below.

Objective: To identify and filter the Microsatellites (SSRs) for the Blueberry 454 unigene assembly

Analyst: Chun-Huai Cheng (Main Bioinformatics Lab), original data from LJ Rowland lab.

Analysis results used in: Rowland et al, 2012, BMC Plant Biology 12:46


1.)  Uploaded file of assembled contigs, 454_blueberry_020311.fasta to the GDR SSR Server

  • Parameters selected = mononucleotides (0), dinucleotides (5), trinucleotides (4), tetranucleotides (3), pentanucleotides (3), hexanucleotides (0)
  • SSR Server results:
Number of input sequences 87071
Number of unique sequences with at least one repeat 17859
Number of unique motifs 608

2.)  Sequences were further filtered to remove sequences that had >2 SSRs or had N's in the primer. (19,808 sequences left)

3.) Primers from Step 2 were compared to the 5,267 dbESTs originally downloaded from NCBI using BLAST. 3,922 sequences are removed due to primers having a match to the current Vaccinium data in the NCBI dbEST. (blastn, e-value = 0.01, ~70% primer length are aligned). This resulted in 15,886 remaining sequences from the analyzed dataset.

4.)  Di- and Tri- nucleotide report was generated for this dataset.

5.)  The SSR containing sequences were annotated with either Swissprot or TrEMBL using BLAST (blastx, e-value cutoff = 1E-6).

6.)  Alternate primers for the remaining sequences are generated.