README.md

Genomics-I-Assignment

Databases

Resource centres:

• The EBI: www.ebi.ac.uk
• The NCBI: www.ncbi.nlm.nih.gov
• UCSC: genome.ucsc.edu

Model organism databases:

• 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

Database building tool:

• www.intermine.org

InterMine databases:

• 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

Ontologies:

• Gene ontology: www.geneontology.org
• Sequence ontology: www.sequenceontology.org

DNA sequence/ genomes:

• Ensembl: www.ensembl.org
• Short read archive: www.ncbi.nlm.nih.gov/sra

Proteins:

• www.uniprot.org
• www.ebi.ac.uk/interpro

RNA:

• rfam.sanger.ac.uk

Pathways:

• www.reactome.org
• www.genome.jp/kegg/

Links for Species

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

Useful Linux Commands

Local databases directory

cd /local/data/public/Genomics_1/assignments/assignment_2

Executables directory

./local/data/public/Genomics_1/programs/[BLAST,genscan,HMMer]

1.1.2 Genscan

Genscan manual:

• http://web.mit.edu/seven/doc/genscan/genscan.txt

1.2.2. HMMER

HMMER tutorials:

• https://bi.snu.ac.kr/Courses/bio02/HMMER_tutorial.pdf
• http://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*