Merton Blackberry Project Description
Reports:
- RH_MEa.genbank.2008-4-4_142537.txt Submission report for GenBank (text format).
- RH_MEa-QualityReport.2008-4-4_142537.xls Report on the quality of the library including overall statistics, plate report, and clone reports. (Excel format).
Library Files:
- RH_MEa.2008-4-4_142537.seq.success.lib Successful, untrimmed sequences (fasta format).
- RH_MEa.2008-4-4_142537.seq.success.qual Successful, untrimmed quality values for above sequences(fasta format).
- RH_MEa.2008-4-4_142537.trim.lib Successful, trimmed quality values for above sequences(fasta format).
- RH_MEa.2008-4-4_142537.trim.qual Successful, trimmed quality values for above sequences(fasta format).
Assembly Files:
- The assembly was created from the trimmed library sequences and their quality values using CAP3 with default parameters.
- RH_MEa.2008-4-4_142537.trim.lib.cap.ace This file can be used to view the contig alignments in Consed (ace format).
- RH_MEa.2008-4-4_142537.trim.lib.cap.aln This is the output from Cap3 with alignments (text format).
- RH_MEa.2008-4-4_142537.trim.lib.cap.contigs Contigs from Cap3 (fasta format).
- RH_MEa.2008-4-4_142537.trim.lib.cap.contigs.qual Quality values for the contigs from Cap3 (fasta format).
- RH_MEa.2008-4-4_142537.trim.lib.cap.singlets Singlets from Cap3 (fasta format).
SSR/Primer Files for Trimmed Sequences:
- The microsatellites were mined using CUGI's in-house repeat finder and Primer3 with default parameters.
- Trimmed Library Results:
- RH_MEa.2008-4-4_142537.trim.lib.SSRs.xls SSRs, primers, alternate primers, summary report and motif frequency report (Excel format).
- RH_MEa.2008-4-4_142537.trim.lib.primer3.output.txt Output file from Primer3 (text format).
- RH_MEa.2008-4-4_142537.trim.lib.sequences.txt File with the sequences containing SSRs (fasta format).
- Contig Results:
- RH_MEa.2008-4-4_142537.trim.lib.cap.contigs.SSRs.xls SSRs, primers, alternate primers, summary report and motif frequency report (Excel format).
- RH_MEa.2008-4-4_142537.trim.lib.cap.contigs.primer3.output.txt Output file from Primer3 (text format).
- RH_MEa.2008-4-4_142537.trim.lib.cap.contigs.sequences.txt File with the sequences containing SSRs (fasta format).
BLAST Result Files:
- BLAST was performed with an E-value cut-off of 1e-5. Only the ten best hits are reported.
- Trimmed Library Results:
- RH_MEa-vs-SwissProt.xls The trimmed RH_MEa sequences run with blastx (6 frame translation of query) against SwissProt downloaded on 10/30/2007 (Excel format).
- RH_MEa-vs-Arabidopsis.xls The trimmed RH_MEa sequences run with blastx (6 frame translation of query) against predicted proteins from the Arabidopsis genome, mips_arabi_all_proteins_v090704 (Excel format).
- Contig Results:
- RH_MEa_contigs-vs-SwissProt.xls The trimmed RH_MEa sequences run with blastx (6 frame translation of query) against SwissProt downloaded on 10/30/2007 (Excel format).
- RH_MEa_contigs-vs-Arabidopsis.xls The trimmed RH_MEa sequences run with blastx (6 frame translation of query) against predicted proteins from the Arabidopsis genome, mips_arabi_all_proteins_v090704 (Excel format).
- RH_MEa_contigs-vs-Rosaceae.xls The trimmed RH_MEa sequences run with tblastx (6 frame translation of query and db) against Rosaceae ESTs downloaded from GenBank on 4/9/2008 (Excel format).
