KSH HW1 Protein analysis

Motif, Pattern, Profiling, Signature

Sequence motif - amino acid sequence pattern that is widespread and has a biological significance

Cf) Structural motif - connectivity between secondary structure elements¹⁾ - The simplest structural motif is a helical bundle

(http://www.proteinstructures.com/Structure/Structure/protein-motifs.html)

Pattern - Characters that appear in common in one protein family

two or more patterns are associated with a single motif ²⁾

Protein Profiling - the detection of the character or quantity of specific sets of proteins

Signature - a part of whole pattern. Short diagnostic pattern that we can find the character of specific protein

1. PROSITE (prosite.expasy.org)

³⁾A protein database which consists of the protein families, domains, functional sites, amino acid patterns and profiles.

They are manually curated by a team of Swiss Institute of Bioinformatics

 

 

 

5. PRINTS (bioinf.man.ac.uk/dbbrowser/PRINTS)

 

PSI-BLAST(blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE=Proteins&PROGRAM=blastp&RUN_PSIBLAST=on)

To search similarity among amino acid sequences . PIR - Protein Informatics Resourse , PSI - Position Specific Iterated

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Reference

*** All these websites are listed in the book called 'Bioinformatics with bioperl' authored by Young-chang Kim

1) http://www.proteinstructures.com/Structure/Structure/protein-motifs.html

2) https://en.wikipedia.org/wiki/Sequence_motif

3) https://en.wikipedia.org/wiki/PROSITE

 

 

Seung-hoon Kim