GCF_000004515.3_V1.1_genomic

The script "BLAST_to_Coding_SSR.R” (https://github.com/soltislab/transcriptome_microsats/blob/master/BLAST_to_Coding_SSR.R) uses a .gff file (annotated Glycine max genome from NCBI), and a BLAST report for SSR Loci blasted against the Glycine max genome to prepare two files, which will be used in a subsequent script (Coding_SSR.py -- https://github.com/soltislab/transcriptome_microsats/blob/master/Coding_SSR.py) to determine which loci are in translated regions of the genome (i.e., regions that are annotated as "CDS"). The output of this script is two files (one contains the SSR loci identified from the BLAST search, with some unncessary columns and duplicates removed, and the other contains the regions of the Glycine max genome that are annotated as "CDS"). This file is the gff file needed for the script

Scaffolds

The Scaffolds.zip file is a compressed zip file containing a directory with the scaffolds corresponding to the microsatellite loci. The Scaffolds directory contains the sequence of the scaffolds that had microsatellites identified on them. The files are bz2 compressed zip files. The unzipped file is a fasta file with all of the scaffolds corresponding to the loci in the LocusInfo directory

G_R_0803-0253-HitTable

The script "BLAST_to_Coding_SSR.R” (https://github.com/soltislab/transcriptome_microsats/blob/master/BLAST_to_Coding_SSR.R) uses a .gff file (annotated Glycine max genome from NCBI), and a BLAST report for SSR Loci blasted against the Glycine max genome to prepare two files, which will be used in a subsequent script (Coding_SSR.py -- https://github.com/soltislab/transcriptome_microsats/blob/master/Coding_SSR.py) to determine which loci are in translated regions of the genome (i.e., regions that are annotated as "CDS"). The output of this script is two files (one contains the SSR loci identified from the BLAST search, with some unncessary columns and duplicates removed, and the other contains the regions of the Glycine max genome that are annotated as "CDS"). This is the third of three files needed to run the script

LocusInfo

The LocusInfo.zip file is a compressed zip file containing a directory with the microsatellite loci for each species. The the LocusInfo directory contains the microsatellite locus information for the 1096 species for which loci were developed. The loci were from the 1KP project (http://onekp.com) transcriptomes. For some species, there were multiple transcriptomes, either from multiple collections or multiple tissues; these have been combined into a single file for each species

glycine_max_454_raw_all

A fasta file is necessary to run pal_finder. The file included here is a fasta file of raw 454 genomic reads from Glycine max (NCBI Trace Archive (TI 1732557604-1733276192; Swaminathan et al., 2007))

G_R_0764-0510-HitTable

The script "BLAST_to_Coding_SSR.R” (https://github.com/soltislab/transcriptome_microsats/blob/master/BLAST_to_Coding_SSR.R) uses a .gff file (annotated Glycine max genome from NCBI), and a BLAST report for SSR Loci blasted against the Glycine max genome to prepare two files, which will be used in a subsequent script (Coding_SSR.py -- https://github.com/soltislab/transcriptome_microsats/blob/master/Coding_SSR.py) to determine which loci are in translated regions of the genome (i.e., regions that are annotated as "CDS"). The output of this script is two files (one contains the SSR loci identified from the BLAST search, with some unncessary columns and duplicates removed, and the other contains the regions of the Glycine max genome that are annotated as "CDS"). This is the second of three files needed to run the script