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Online Biology Research Tools

22-Jul-2019
Online Biology Research Tools

 

As a crucial component of GeneTex’s antibody development program, the R&D team assiduously reviews the pertinent literature in conjunction with other biomedical research media and has bookmarked a collection of useful online tools. Like NCBI, Ensembl, and UniProt, these sites are of great value to the entire research community. We are happy to provide this listing.

 

BLAST

blastp: blast protein sequence in protein databases (NCBI).

tblastn: blast protein sequence in translated nucleotide databases (NCBI).

blastn: blast nucleotide sequence in nucleotide databases (NCBI).

blastx: blast translated nucleotide sequence in protein databases (NCBI).

SMARTBLAST: search a protein query against 27 genomes spanning a wide taxonomic range for homolog analysis (NCBI).

Sequence Analysis

ScanProsite: identify protein families, domains, functional sites, and modifications.

Compute pI/Mw: compute theoretical isoelectric point and molecular weight of a given protein sequence (ExPASy).

Three-/ one-letter code: convert three letter translations to one letter translations and inversely.

EMBOSS Transeq: translate DNA or RNA to the corresponding peptide sequence in various frame settings (EMBL-EBI).

EMBOSS Backtranseq: reads a protein sequence and writes the nucleic acid sequence it is most likely to have come from (EMBL-EBI).

Alignment

COBALT: align two or more protein sequences (NCBI).

Clustal Omega: align three or more protein/DNA/RNA sequences (EMBL-EBI).

MUSCLE: align multiple protein/DNA sequences (EMBL-EBI).

Expression Pattern

The Human Protein Atlas: shows expression profiles of human genes and proteins across major organs, tissues, and cell lines.

Expression Atlas: gene expression across species and biological conditions.

LifeMap Discovery: compendium of information/tools related to embryonic and differentiated cells and tissues.

Primer Design

Primer3: pick primers from a DNA sequence with intended primer size, Tm, and GC%.

Primer-BLAST: check specificity of a primer pair.

Primer analysis: analyze Tm, length, GC%, and MW of a primer sequence in basic or special salt conditions.

3D Structure Modeling

SWISS-MODEL: model protein 3D structure by entering a protein sequence.