Computer programs

Question 1

Ensemble

Answer 1

Genome browser of multiple types of organisms. Used to extract sequences and analyse things at the nucleotide level.

Question 2

NCBI BLAST

Answer 2

NCBI = National Center for Biotechnology Information
BLAST= Basic Local Alignment Search Tool
Blast searches help you identify and compare sequences from various sources:

• blast n (nucleotide databases)
• blast p (protein database)
• t blast n (translated nucleotide database using a nucleotide query)
• blast x (protein databases using a translated nucleotide)
• tblast c (translated nucleotide database using translated nucleotide query)

Question 3

NCBI primer-BLAST

Answer 3

Designing primers for amplifying sequences.

It looks for regions in a target sequence that fit certain primer parameters (which the user can adjust if they would like) and then checks (via BLAST) to make sure that they are specific. You can also provide primer sequences of your own and it will run just the BLAST to tell you which sequences might be amplified using that primer pair.

Question 4

A Plasmid Editor (ApE)

Answer 4

Used for cloning…This helps you to plan cloning projects and to “mark-up” sequences with your own notes

Question 5

Brain RNA-seq

Answer 5

database of bulk RNA-Seq data collected from human and mouse brain cells. You can search for a gene of interest to see which brain cell types it is expressed in.

Question 6

GTEx

Answer 6

Genotype-Tissue Expression project is a resource that collects data about gene expression across different tissues and cell types (focuses only on human genes)

Question 7

OMIM

Answer 7

Online Mendelian Inheritance in Man
Database of information on human diseases and disease-causing genes
focuses on human disease, but includes information from all sources, including in vivo and in vitro analyses

Question 8

gnomAD

Answer 8

GeNOMe Aggregation Database:
Collects human exome and genome sequencing data.
Useful for checking whether or not a patient variant might be pathogenic by seeing how often it has already been reported and comparing to other reported variants in the same gene.

Question 9

Zfin

Answer 9

ZebraFish Information Network is a database for all things zebrafish. You can search or browse for information about gene expression, transgenic or mutant lines, anatomy, protocols, publications etc.

Question 10

Clusta Omega

Answer 10

Multiple sequence aligner

This tool can be used to align three or more RNA, DNA, or protein sequences (of the same type).

Question 11

addgene

Answer 11

Plasmid database and online resource for molecular biology

Question 12

NEB tm calculator

Answer 12

determine annealing temperature for your primer pair (PCR)

Question 13

NEBcloner

Answer 13

Restriction enzyme digest tool:
to determine compatibility of restriction enzymes