DATA BASE SEKUENS

Aprilia Indra Kartika, M.Biotech

Cakuman Materi
• Definisi Database
• Sekuen dan Atributnya
• Berbagai Format Sekuen
• Fasta
• Flat File
• SAM/ BAM
• GenBank
• Database Molekuler yang Penting
• Database Primer
• Database Sekunder
Definisi Database
• Repository umum yang memuat informasi data genom manusia atau
makhluk hidup, cloning, polymorfisme dan maps. Genome database
memiliki hubungan antara satu database dengan yang lainnya, sitasi
literature, untuk mengentri pada database lain, termasuk database
sekuens.

• GDB, http://www.gdb.org
• https://www.genome.jp/kegg/genome.html
• https://www.ncbi.nlm.nih.gov/genome
• https://genome.ucsc.edu/
• http://asia.ensembl.org/index.html
Sekuens dan atributnya
• Sekuens merupakan urutan basa nukleotida DNA.
Bioinformatics beneficials

• Use of Bioinformatics
• DNA analysis – Genome sequencing
• Sequence assembly
• Sequence/gene annotations
• Genefinding/Sequence translation tools
• Sequence Similarity searching (eg. BLAST, ClustalW)
• Comparison between genomes
• Evolution of sequences (Phylogenetic analysis)
• Gene expression
Use of Bioinformatics
• Protein analysis – Structure • X-ray crystallography • Homology based
models • Drug designing – Sequence • Sequence similarity • Protein
family assignments • Conserved motifs • Proteomics data analysis •
Protein Evolution.

• Other uses: – Drug designing – Vaccine development – Dairy

technology – Forensics – Crop improvement – Designing enzymes for
detergents – Genetic counseling
Recent events making bioinformatics more
important
• Exponential expansion of biological information
• Expansion of multiple types of information
• Cheaper high throughput technologies
• Improvement in computation power
• Lack of standards/quality
• Need for micro and macro analysis
• Need for better algorithms
Bioinformatics Analysis? It is like any other lab
analysis!
• You need to know your data/input sources
• You need to understand your methods and their assumptions
• You need a plan to get from point A to point B
• You need to understand your equipment
• You need to be critical and understand potential sources of error
• You need to interpret your results
• Your results need to be reproducible
• Your results should be testable
References
• http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html •
http://icgeb.res.in/whotdr
•http://en.wikipedia.org/wiki/Bioinformatics
• Baxevanis & Ouellette 2001. Bioinformatics: A Practical Guide to the
Analysis of Genes and Proteins 2nd Edition. John Wiley Publishing.
• Gibas & Jambeck 2001. Developing Bioinformatics Computer Skills.
O’Reilly.
• Bioinformatics: Genome Sequence Analysis Mount 2001
• Bioinformatics For Dummies – Claverie & Notredame 2003
• Introduction to Bioinformatics – Lesk 2002