- The EBI: www.ebi.ac.uk
- The NCBI: www.ncbi.nlm.nih.gov
- UCSC: genome.ucsc.edu
- Budding yeast: www.yeastgenome.org
- Worm: www.wormbase.org
- Fly: www.flybase.org
- Mouse: www.informatics.jax.org
- Rat: rgd.mcw.edu
- Zebrafish: zfin.org
- www.flymine.org
- intermine.modencode.org
- ratmine.mcw.edu
- yeastmine.yeastgenome.org
- www.metabolicmine.org
- www.flytf.org
- mitominer.mrc-mbu.cam.ac.uk
- targetmine.nibio.go.jp
- Gene ontology: www.geneontology.org
- Sequence ontology: www.sequenceontology.org
- Ensembl: www.ensembl.org
- Short read archive: www.ncbi.nlm.nih.gov/sra
- rfam.sanger.ac.uk
| Species | UniProt Reference Proteome |
|---|---|
| D. sechelli | https://www.uniprot.org/proteomes/UP000001292 |
| D. yakuba | https://www.uniprot.org/proteomes/UP000002282 |
| D.pseudoobscura | https://www.uniprot.org/proteomes/UP000001819 |
| D. mojavensis | https://www.uniprot.org/proteomes/UP000009192 |
Local databases directory
cd /local/data/public/Genomics_1/assignments/assignment_2
Executables directory
./local/data/public/Genomics_1/programs/[BLAST,genscan,HMMer]
Genscan manual:
HMMER tutorials:
- https://bi.snu.ac.kr/Courses/bio02/HMMER_tutorial.pdf
- https://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf
Navigate to where HMMER programs are installed
cd /local/data/public/Genomics_1/programs/hmmer-3.3/bin/bin
Run HMMER on each fly database
hmmsearch /local/data/public/Genomics_1/assignments/assignment_2/pfam_database/Pfam-A.hmm /home/tw556/Documents/Genomics_1/Assignment_2/Proteins/drosophila_mojavensis.fasta > /home/tw556/Documents/Genomics_1/Assignment_2/Proteins/mojavensis_hmmer.txt
hmmsearch /local/data/public/Genomics_1/assignments/assignment_2/pfam_database/Pfam-A.hmm /home/tw556/Documents/Genomics_1/Assignment_2/Proteins/drosophila_pseudoobscura_proteins.fasta > /home/tw556/Documents/Genomics_1/Assignment_2/Proteins/pseudoobscura_hmmer.txt
hmmsearch /local/data/public/Genomics_1/assignments/assignment_2/pfam_database/Pfam-A.hmm /home/tw556/Documents/Genomics_1/Assignment_2/Proteins/drosophila_yakuba_proteins.fasta > /home/tw556/Documents/Genomics_1/Assignment_2/Proteins/yakuba_hmmer.txt
hmmsearch /local/data/public/Genomics_1/assignments/assignment_2/pfam_database/Pfam-A.hmm /home/tw556/Documents/Genomics_1/Assignment_2/Proteins/drosophila_sechellia.fasta > /home/tw556/Documents/Genomics_1/Assignment_2/Proteins/sechellia_hmmer.txt
PFAM pfam2go.tab*