14

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https://web.expasy.org/docs/swiss-­prot_guideline.html

takes the interested person to this link. As explained on the page, there are also detailed

comments on the sequence here. These so-called “header entries” provide a wealth of

information about protein sequences, followed by the actual sequence.

How Do I Quickly Analyze Protein Data?

The ExPASy site brings expert help to get started with protein analysis. “Proteomics”

means the analysis of large amounts (“omics”) of protein data.

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https://www.expasy.org/proteomics

In addition to various databases, you can also find a lot of bioinformatics informa­

tion here:

Proteomics

Large-scale analyses of proteins

Protein sequences

and identification

Identification of proteins by sequence

Mass spectrometry

and 2-DE data

Identification of peptides found in mass spectroscopy or protein spots

found in 2D gel. Evaluation software and databases for these steps

Protein

characterisation and

function

Domain analyses in particular

Families, patterns

and profiles

Proteins with the same function form a family. In particular, always the

same (“conserved”) amino acids, patterns and position-specific

frequencies of amino acids for these families are summarized here

Post-translational

modification

After production at the ribosome, proteins are further modified, these are

the post-translational modifications

Protein structure

Finding or calculating the three-dimensional protein structure. A fast

homology prediction via the SWISS-MODEL server is also offered here

Protein-protein

interaction

Predicting which protein interacts with which other protein

Similarity search/

alignment

There are also a number of alternatives to BLAST here. Multiple protein

sequences can also be compared

Genomics

How are the associated genes related to the proteins they encode?

Structural

bioinformatics

In particular, the properties of protein structures are determined, for

example globular proteins are particularly soluble

Systems biology

A nice introductory page on system effects of proteins, for example

protein signalling cascades and phosphatases to switch off such signals

Phylogeny/evolution

Proteins develop according to specific patterns; in particular, building

units, the protein domains, are assembled to form new proteins

Population genetics

How are important proteins and protein properties distributed in a

population? What are the different types?

Transcriptomics

How are protein and its coding mRNA related?

(continued)

1  Sequence Analysis: Deciphering the Language of Life