Molecule Tutorials - Herong's Tutorial Examples

∟INSDC (International Nucleotide Sequence Database Collaboration)

∟RefSeq Proteins of Human Genome

This section provides a tutorial example on how to download the RefSeq Proteins data file, which containes 59,248 human proteins in FASTA format.

What Is RefSeq Proteins of Human Genome? - RefSeq Proteins of Human Genome is a data file in FASTA format that contains about 60,000 human protein sequences provided by NCBI (National Center for Biotechnology Information.

Here is what I did to download the RefSeq Proteins of Human Genome data file.

1. Get the data file with "curl" command: 

herong$ curl ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation\
  /GRCh38_latest/refseq_identifiers/GRCh38_latest_protein.faa.gz > proteins.gz

2. Unzip and verify the file. 

herong$ gunzip proteins.gz

herong$ head -100 proteins
>NP_000005.3 alpha-2-macroglobulin isoform a precursor [Homo sapiens]
MGKNKLLHPSLVLLLLVLLPTDASVSGKPQYMVLVPSLLHTETTEKGCVLLSYLNETVTVSASLESVRGNRSLFTDLEAE
NDVLHCVAFAVPKSSSNEEVMFLTVQVKGPTQEFKKRTTVMVKNEDSLVFVQTDKSIYKPGQTVKFRVVSMDENFHPLNE
LIPLVYIQDPKGNRIAQWQSFQLEGGLKQFSFPLSSEPFQGSYKVVVQKKSGGRTEHPFTVEEFVLPKFEVQVTVPKIIT
ILEEEMNVSVCGLYTYGKPVPGHVTVSICRKYSDASDCHGEDSQAFCEKFSGQLNSHGCFYQQVKTKVFQLKRKEYEMKL
HTEAQIQEEGTVVELTGRQSSEITRTITKLSFVKVDSHFRQGIPFFGQVRLVDGKGVPIPNKVIFIRGNEANYYSNATTD
EHGLVQFSINTTNVMGTSLTVRVNYKDRSPCYGYQWVSEEHEEAHHTAYLVFSPSKSFVHLEPMSHELPCGHTQTVQAHY
ILNGGTLLGLKKLSFYYLIMAKGGIVRTGTHGLLVKQEDMKGHFSISIPVKSDIAPVARLLIYAVLPTGDVIGDSAKYDV
ENCLANKVDLSFSPSQSLPASHAHLRVTAAPQSVCALRAVDQSVLLMKPDAELSASSVYNLLPEKDLTGFPGPLNDQDNE
DCINRHNVYINGITYTPVSSTNEKDMYSFLEDMGLKAFTNSKIRKPKMCPQLQQYEMHGPEGLRVGFYESDVMGRGHARL
VHVEEPHTETVRKYFPETWIWDLVVVNSAGVAEVGVTVPDTITEWKAGAFCLSEDAGLGISSTASLRAFQPFFVELTMPY
SVIRGEAFTLKATVLNYLPKCIRVSVQLEASPAFLAVPVEKEQAPHCICANGRQTVSWAVTPKSLGNVNFTVSAEALESQ
ELCGTEVPSVPEHGRKDTVIKPLLVEPEGLEKETTFNSLLCPSGGEVSEELSLKLPPNVVEESARASVSVLGDILGSAMQ
NTQNLLQMPYGCGEQNMVLFAPNIYVLDYLNETQQLTPEIKSKAIGYLNTGYQRQLNYKHYDGSYSTFGERYGRNQGNTW
LTAFVLKTFAQARAYIFIDEAHITQALIWLSQRQKDNGCFRSSGSLLNNAIKGGVEDEVTLSAYITIALLEIPLTVTHPV
VRNALFCLESAWKTAQEGDHGSHVYTKALLAYAFALAGNQDKRKEVLKSLNEEAVKKDNSVHWERPQKPKAPVGHFYEPQ
APSAEVEMTSYVLLAYLTAQPAPTSEDLTSATNIVKWITKQQNAQGGFSSTQDTVVALHALSKYGAATFTRTGKAAQVTI
QSSGTFSSKFQVDNNNRLLLQQVSLPELPGEYSMKVTGEGCVYLQTSLKYNILPEKEEFPFALGVQTLPQTCDEPKAHTS
FQISLSVSYTGSRSASNMAIVDVKMVSGFIPLKPTVKMLERSNHVSRTEVSSNHVLIYLDKVSNQTLSLFFTVLQDVPVR
DLKPAIVKVYDYYETDEFAIAEYNAPCSKDLGNA
>NP_000006.2 arylamine N-acetyltransferase 2 [Homo sapiens]
MDIEAYFERIGYKNSRNKLDLETLTDILEHQIRAVPFENLNMHCGQAMELGLEAIFDHIVRRNRGGWCLQVNQLLYWALT
...

3. Count number of proteins. The output shows that 59,248 proteins have been recorded in the data file. 

herong$ grep ">NP_" proteins | wc
  59248  511098 4345961

Table of Contents

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Molecule Mass and Weight

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 DNA Sequencing

 Gene Mutation

 SDF (Structure Data File)

 PyMol Installation

 PyMol GUI and CLI

 PyMol Selections

 PyMol Editing Functions

 PyMol Measurement Functions

 PyMol Movie Functions

 PyMol Python Integration

 PyMol Object Functions

 ChEMBL Database - European Molecular Biology Laboratory

 PubChem Database - National Library of Medicine

 PDB (Protein Data Bank)

►INSDC (International Nucleotide Sequence Database Collaboration)

 What Is INSDC

 Reference Genome Sequence Data File

►RefSeq Proteins of Human Genome

 HGNC (HUGO Gene Nomenclature Committee)

 Relocated Tutorials

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB