LEMONS Database Generator GUI

Transcription

1 LEMONS Database Generator GUI For more details and updates : If you have any questions or requests, please contact us by lemons.help@gmail.com

2 Part : Using the Ensembl Data Source In this part we will generate an A.thaliana database that can be used by LEMONS. Important notes: Blast needs to be installed in order for LEMONS and LEMONS Database Generator to work. For more details, see: LEMONS directory needs to be located on a local drive. The genome files and the annotation files should not be in the same directory. Follow the numbered arrows.

3 The New Database Name A.Thaliana 2 A.Thaliana 4 3. Double click on the START_LEMONS_Database_Generator_GUI.bat 2. Click on the Enter button. 3. Enter the new database name. 4. Click on the OK button. 5. Click on the Ensembl radio button. 5

4 Ensembl Data Source Ensembl Plants: Ensembl: Click on the link.

5 Download Genome. Click on the link.

6 Genome Files LEMONS Database Generator can receive one or multiple genome files (.fa.gz or.2bit) A.Thaliana C:\Genomes 2. Download the genome files to a new directory. 2. Click on the Select button and select the directory containing the genome files.

7 Gene Annotation Files More GFF3s can also be found at ftp://ftp.ensembl.org/pub/release-8/gff3/. Click on the link.

8 Gene Annotation Files A.Thaliana C:\Genomes E:\Arabidopsis_thaliana.TAIR0.27.gff3.gz. Download the GFF3 file to a new annotation directory. 2. Click on the Select button and select the GFF3 file.

9 Gene Annotation Files. Click on the link. 2. Click on the link. 2

10 Gene Annotation Files A.Thaliana C:\Genomes E:\Arabidopsis_thaliana.TAIR0.27.gff3.gz E:\Arabidopsis_thaliana.TAIR0.27.pep.all.fa.gz +2. Download the pep.all.fa.gz file to the annotation directory. 2. Click on the Select button and select the pep.all.fa.gz file.

11 Database Generation A.Thaliana C:\Genomes E:\Arabidopsis_thaliana.TAIR0.27.gff3.gz E:\Arabidopsis_thaliana.TAIR0.27.pep.all.fa.gz. Click on the Generate Database button.

12 Database Generation. Double click on the START_LEMONS_GUI.bat Another genome database has been added.

13 Part 2 : Using the UCSC Genome Data Source In this part we will generate a C.elegans database that can be used by LEMONS. Important notes: Blast needs to be installed in order for LEMONS and LEMONS Database Generator to work. For more details, see: LEMONS directory needs to be located on a local drive. The genome files and the annotation files should not be in the same directory. Follow the numbered arrows.

14 The New Database Name C.elegans 2 C.elegans 4 3. Double click on the START_LEMONS_Database_Generator _GUI.bat 2. Click on the Enter button. 3. Enter the new database name. 4. Click on the OK button. 5. Click on the UCSC radio button. 5

15 UCSC Genome Data Source Click on the link. 2. Click on the link. 2

16 Genome Download C.elegans C:\Genomes 2. Download the genome file (.2bit) to a new directory. 2. Click on the Select button and select the directory containing the genome file.

17 Gene Annotation Files 2. Click on the Tables tab. Make sure all fields are as shown. 2. Click on the get output button and save the file to a new annotation directory.

18 Gene Annotation Files Make sure all fields are as shown.. Click on the get output button and save the file to the annotation directory.

19 Database Generation C.elegans C:\Genomes E:\KnownGenes E:\Pep 2 3. Click on the Select button and select the KnownGenes annotation file. 2. Click on the Select button and select the Pep annotation file. 3. Click on the Generate Database button.

20 Database Generation. Double click on the START_LEMONS_GUI.bat Another genome database has been added.

21 Using RefSeq Database Make sure all fields are as shown.. Click on the get output button and save the file to the annotation directory.

22 Using RefSeq Database C.elegans C:\Genomes E:\refGenes 2. Click on the Select button and select the refgenes annotation file. Leave the Peptides File Location field empty. 2. Click on the Generate Database button.