Formats de données en biologie

Formats de données
en biologie
Pierre Poulain
pierre.poulain@univ-paris-diderot.fr

09/2011

Menu
1 Rappels

2 Problématique

3 Séquences

4 Structures

5 Quelques précautions

6 Conclusion

7 Références & crédits graphiques
PP Université Paris Diderot - Paris 7 2

Menu
1 Rappels

2 Problématique

3 Séquences

4 Structures


6 Conclusion


Dogme de la biologie

ADN ARN protéine

transcription traduction


Menu
1 Rappels

2 Problématique

3 Séquences

4 Structures


6 Conclusion


Expérimentalement
ADN ARN protéine
A,T,C,G A,U,C,G V,G,W,C...

AAGATGACCGTGTGTCAT
TTGATCCTGAACTGTTTG
AAAAAATGTTCCGTGACG
GACTCTTTGATGATGAGA
CCTCGGAAGTAACGGAGC
AGCGCAATGTTCCGTGAC
CAGCTGACAATGTATCAG
ATTCCAGACTGGATCAGA
TCTGAATGCCATTAGCTT

TTGTCACCTGTACACTGGCATTACTACACAGAAACCCAGATGTCCGTTACC
Séquences > structures
AAGATGACCGTGTGTCATTCATTCCTAAGATTCAAAATGATTTCGATGGCA
TTGATCCTGAACTGTTTGAATTGAGAAAAGCTGTTATGGACACCAATGAAA
AAAAAATGTTCCGTGACGACACTTTCGGCAAGAACCTGAATGCAAACACAA
GACTCTTTGATGATGAGACTAGTTCATCCTCTTTTAAGCAAAATTCCTCTC
CCTCGGAAGTAACGGAGCAACCTGTGCAACCAACCTCCGCTGTCATGGGTA
GCTTCTTGTCTCCACAGTACCAACGTGCGTCATCTGCTTCTCGTACTAATC
ATAATACAAGCACCTCCAGTTTAATGAAGCCTGAATCAAGTCTCTACCTGG
ATAAATCATATTCGCATTTTAACAACAACGGCAGCAACGAAAACGCCCGCA
CATATTTGTAATCCAATATATACTCACATGTAACAACTTATTATATAAATA
AAGGATATCCTACATTATATTTCATAGAAAACCGCTCAAAAAGGTGTATTA
CATCCCAACACCACACATATTTCAGCGATAAAAACCTTAAATGTGAAATTC
CTGCTTCCTTAAATGTACGCAATTGCCGCTTTTTTCTGACATCTTTTTTGA
AAGGAAACAGATCCTCCAGAAGGGATTTACTGTTGGCTATTTTGTGTTAGA
ATAATAGATTAGGTTGCGTAAGTCATGGTCGAAAATAGTACGCAGAAGGCC
GGAAATGATGATAATAGCTCTACCAAGCCATATTCGGAGGCGTTTTTCTTA
AACCCAACGCCTGGATTAGAAGCTGAGCACTCAAGCACATCGCCTGCCCCC
AACTTGAAAATCGGTATGCTATTATCAATGCTTTACAATTCTGTCGGTTAC
GAGGATCATTGCCCTCAAGGTGGCGAATATTCGGATTTATTGAGAAATTTG
TGTGAAGCTATTTTGCCATCTTACGAAATTATTGAACGCTACAAGAACCAC

Menu
1 Rappels

2 Problématique

3 Séquences

4 Structures


6 Conclusion


Séquences
nucléiques, protéiques


Format Fasta

Le plus simple

>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
IENY


Fasta

>en-tête
séquence sur 80 caractères maximum par ligne
séquence sur 80 carac


Remarques

> colle en-tête

longueur de chaque ligne ﬁxée

extensions .fasta, .seq, .fas, .fna, .faa

Python : chaînes de caractères + listes
+ (biopython)


Multifasta
>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
IENY
>gi|134252438|gb|ABO64984.1| cytochrome b [Elephantulus rupestris]
TAFSSVTHICRDVNYGWLIRYLHANGASLFFICLFIHVGRGIYYGSYLYFETWNIGVILLFITMATAFMG
YVLPWGQMSFWGATVITNLLSAIPYIGTTLVEWIWGGFSVDKATLTRFFAFHFILPFIIAALAMVHLLFL
HETGSNNPLGLVSDSDKIPFHPYYTIKDLLGVFAILILHLSLVLFSPDLLGDPDNYTPANPLNTPPHIKP
EWYFLFAYAILRSIPNKLGGVLALVLSILILIIFPLLHTSKQRSLMFRPISQCLFWVLVADLLTLTWIGG
QPVEHPYIIIGQLASILYFTIILVLMPIAGVIENHIIKL
>gi|157367467|gb|ABV45600.1| cytochrome b [Mammuthus primigenius]
MTHIRKSHPLLKIINKSFIDLPTPSNISTWWNFGSLLGACLITQILTGLFLAMHYTPDTMTAFSSMSHIC
RDVNYGWIIRQLHSNGASIFFLCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSF
WGATVITNLFSAIPYIGTDLVEWIWGGFSVDKATLNRFFALHFILPFTMIALAGVHLTFLHETGSNNPLG
LTSDSDKIPFHPYYTIKDFLGLLILILLLLLLALLSPDMLGDPDNYMPADPLNTPLHIKPEWYFLFAYAI
LRSVPNKLGGILALLLSILILGMMPLLHTSKHRSMMLRPLSQVLFWTLATDLLMLTWIGSQPVEHPYIII
GQMASILYFSIILAFLPIAGMIENYLIK


Bases de données de séquences
primaires

GenBank – EMBL – DDBJ


GenBank http://www.ncbi.nlm.nih.gov/

Exemple
LOCUS NM_001001317 940 bp mRNA linear PRI 27-DEC-2010
DEFINITION Homo sapiens trypsin X3 (TRYX3), mRNA.
ACCESSION NM_001001317
VERSION NM_001001317.2 GI:170650697
[...]

FEATURES Location/Qualifiers
source 1..940
/organism="Homo sapiens"
/mol_type="mRNA"
/db_xref="taxon:9606"
/chromosome="7"
/map="7q34"
gene 1..940
/gene="TRYX3"
/gene_synonym="FLJ16649; MGC35022; PRSS1; TRY1; UNQ2540"
/note="trypsin X3"
/db_xref="GeneID:136541"
/db_xref="HPRD:15572"
[...]

ORIGIN
1 aaggctggca aaaaggagac cagacaggag gcgtctgtag agatatcatg aacttcaact
61 tagctttgtt ttccagagac tggagctaaa ctgggctttc aacatcatca tgaagtttat
[...]
781 tgccaaaatt ttttactata taccctggat tgaaaatgta atccaaaata actgagctgt
841 ggcagttgtg gaccatatga cacagcttgt ccccatcgtt cacctttaga attaaatata
901 aattaactcc tcaaaaaaaa aaaaaaaaaa aaaaaaaaaa
//


Exemple
DEFINITION
ACCESSION
VERSION
Homo sapiens trypsin X3 (TRYX3), mRNA.
NM_001001317
NM_001001317.2 GI:170650697
en-tête
[...]

source 1..940
/organism="Homo sapiens"
/mol_type="mRNA"
/chromosome="7"

gene
/map="7q34"
1..940
features
/gene="TRYX3"
/note="trypsin X3"
[...]

ORIGIN

[...]
séquence
//


En-tête
| | | | |
nom taille type de division date de
molécule modification

ACCESSION NM_001001317
|
numéro d'accession (unique et stable)

SOURCE Homo sapiens (human)
|
nom de l'organisme

ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
|
taxonomie

REFERENCE 1 (bases 1 to 940)
AUTHORS Bubb,K.L., Bovee,D., Buckley,D., Haugen,E., Kibukawa,M.,
Paddock,M., Palmieri,A., Subramanian,S., Zhou,Y., Kaul,R., Green,P.
and Olson,M.V.
TITLE Scan of human genome reveals no new Loci under ancient balancing
selection
JOURNAL Genetics 173 (4), 2165-2177 (2006)
PUBMED 16751668
|
référence bibliographique


Features
début et fin du gène
| nom du gène
gene 1..940 |
/gene="TRYX3"
/note="trypsin X3"
|
identifiants d'autres bases de données
séquence codante début et fin
| |
CDS 110..835
/gene="TRYX3"
/EC_number="3.4.21.4"
/note="trypsin-X3" nom de la protéine produite
/codon_start=1 |
/product="trypsin-X3 precursor"
/protein_id="NP_001001317.1"
/db_xref="GI:48255915"
/db_xref="CCDS:CCDS5871.1"
/translation="MKFILLWALLNLTVALAFNPDYTVSSTPPYLVYLKSDYLPCAGV
LIHPLWVITAAHCNLPKLRVILGVTIPADSNEKHLQVIGYEKMIHHPHFSVTSIDHDI
MLIKLKTEAELNDYVKLANLPYQTISENTMCSVSTWSYNVCDIYKEPDSLQTVNISVI
SKPQCRDAYKTYNITENMLCVGIVPGRRQPCKEVSAAPAICNGMLQGILSFADGCVLR
ADVGIYAKIFYYIPWIENVIQNN"
|
séquence de la protéine


Séquence

ORIGIN
121 cctcctctgg gccctcttga atctgactgt tgctttggcc tttaatccag attacacagt
181 cagctccact cccccttact tggtctattt gaaatctgac tacttgccct gcgctggagt
241 cctgatccac ccgctttggg tgatcacagc tgcacactgc aatttaccaa agcttcgggt
301 gatattgggg gttacaatcc cagcagactc taatgaaaag catctgcaag tgattggcta
361 tgagaagatg attcatcatc cacacttctc agtcacttct attgatcatg acatcatgct
421 aatcaagctg aaaacagagg ctgaactcaa tgactatgtg aaattagcca acctgcccta
481 ccaaactatc tctgaaaata ccatgtgctc tgtctctacc tggagctaca atgtgtgtga
541 tatctacaaa gagcccgatt cactgcaaac tgtgaacatc tctgtaatct ccaagcctca
601 gtgtcgcgat gcctataaaa cctacaacat cacggaaaat atgctgtgtg tgggcattgt
661 gccaggaagg aggcagccct gcaaggaagt ttctgctgcc ccggcaatct gcaatgggat
721 gcttcaagga atcctgtctt ttgcggatgg atgtgttttg agagccgatg ttggcatcta
// |
séquence du gène


Remarques
extension .gbk

visualisation : artemis
http://www.sanger.ac.uk/resources/software/artemis/

format EMBL (.embl) ∼ .gbk

Python : chaînes de caractères/listes
+ expressions régulières


EMBL
ID 7 standard; DNA; HTG; 5916 BP.
AC chromosome:GRCh37:7:141951963:141957878:-1
[...]
OS Homo sapiens (human)
OC Eukaryota; Metazoa; Eumetazoa; Bilateria; Coelomata; Deuterostomia;
OC Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi;
OC Sarcopterygii; Tetrapoda; Amniota; Mammalia; Theria; Eutheria;
OC Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini;
OC Hominoidea; Hominidae; Homininae; Homo.
[...]
FT gene 1..5916
FT /gene=ENSG00000171147
FT /locus_tag="U66059.56"
FT /note="Trypsin-X3 Precursor (EC 3.4.21.4)
[...]
FT CDS join(352..391,2386..2524,2748..3004,5448..5587,5689..5838)
FT /gene="ENSESTG00000027201"
FT /protein_id="ENSESTP00000068598"
FT /note="transcript_id=ENSESTT00000068598"
FT /translation="MKFILLWALLNLTVALAFNPDYTVSSTPPYLVYLKSDYLPCAGVL
FT IHPLWVITAAHCNLPKLRVILGVTIPADSNEKHLQVIGYEKMIHHPHFSVTSIDHDIML
[...]
SQ Sequence 5916 BP; 1714 A; 1266 C; 1022 G; 1914 T; 0 other;
AAGGCTGGCA AAAAGGAGAC CAGACAGGAG GCGTCTGTAG AGATATCATG AACTTCAACT 60
TAGCTTTGGT ACTTTCTTCC CTGAAGACAG AGGGCAGAAC TCTGAGTTCC AGAACCATTT 120
TCAACTGTAT TGGGGACCAA TCACTTGACT CTATTCTTGT CTCTCTGACA GATGACGCTA 180
CACTCTCCTC TGAATAATGG ACACCATTTC TAAAACTGAA TCCTGCTACT AAAATAATTC 240
[...]
GTAATCCAAA ATAACTGAGC TGTGGCAGTT GTGGACCATA TGACACAGCT TGTCCCCATC 5880
GTTCACCTTT AGAATTAAAT ATAAATTAAC TCCTCA 5916
//


Bases de données de séquences
secondaires

UniProt – Pfam – ProSite – ...


UniProt http://www.uniprot.org/

Exemple
ID TRY3_HUMAN Reviewed; 304 AA.
AC P35030; A9Z1Y4; P15951; Q15665; Q5VXV0; Q9UQV3;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 14-OCT-2008, sequence version 2.
DT 11-JAN-2011, entry version 111.
DE RecName: Full=Trypsin-3;
DE EC=3.4.21.4;
DE AltName: Full=Brain trypsinogen;
DE AltName: Full=Mesotrypsinogen;
[...]
CC -!- FUNCTION: Digestive protease specialized for the degradation of
CC trypsin inhibitors.
CC -!- CATALYTIC ACTIVITY: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.
CC -!- COFACTOR: Binds 1 calcium ion per subunit.
[...]
DR PIR; S33496; S33496.
DR RefSeq; NP_002762.2; NM_002771.3.
DR UniGene; Hs.654513; -.
DR PDB; 1H4W; X-ray; 1.70 A; A=81-304.
[...]
FT DISULFID 196 263
FT DISULFID 228 242
FT DISULFID 253 277
[...]
SQ SEQUENCE 304 AA; 32529 MW; 4C4303C310B7BFFC CRC64;
MCGPDDRCPA RWPGPGRAVK CGKGLAAARP GRVERGGAQR GGAGLELHPL LGGRTWRAAR
DADGCEALGT VAVPFDDDDK IVGGYTCEEN SLPYQVSLNS GSHFCGGSLI SEQWVVSAAH
CYKTRIQVRL GEHNIKVLEG NEQFINAAKI IRHPKYNRDT LDNDIMLIKL SSPAVINARV
STISLPTTPP AAGTECLISG WGNTLSFGAD YPDELKCLDA PVLTQAECKA SYPGKITNSM
FCVGFLEGGK DSCQRDSGGP VVCNGQLQGV VSWGHGCAWK NRPGVYTKVY NYVDWIKDTI
AANS
//


Détails
ID TRY3_HUMAN Reviewed; 304 AA.
| | |
nom origine : Swiss-Prot taille

DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 14-OCT-2008, sequence version 2.
DT 11-JAN-2011, entry version 111.
|
dates d'entrée dans UniProt, de modification de la séquence, de modification de la fiche

DE RecName: Full=Trypsin-3;
|
nom de la protéine

DE AltName: Full=Brain trypsinogen;
DE AltName: Full=Mesotrypsinogen;
DE AltName: Full=Serine protease 3;
DE AltName: Full=Serine protease 4;
DE AltName: Full=Trypsin III;
|
noms alternatifs

OS Homo sapiens (Human).
|
organisme

OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
|
taxonomie


Détails (2)
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS A AND B), AND VARIANT ALA-188.
RC TISSUE=Brain;
RX MEDLINE=94123994; PubMed=8294000; DOI=10.1016/0378-1119(93)90460-K;
RA Wiegand U., Corbach S., Minn A., Kang J., Mueller-Hill B.;
RT "Cloning of the cDNA encoding human brain trypsinogen and
RT characterization of its product.";
RL Gene 136:167-175(1993).
|
référence bibliographique

CC -!- FUNCTION: Digestive protease specialized for the degradation of
CC trypsin inhibitors.
CC -!- CATALYTIC ACTIVITY: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.
CC -!- COFACTOR: Binds 1 calcium ion per subunit.
CC -!- SUBCELLULAR LOCATION: Secreted.
|
annotations (fonction, localisation)

DR PIR; S12764; S12764.
DR PIR; S33496; S33496.
DR RefSeq; NP_002762.2; NM_002771.3.
DR UniGene; Hs.654513; -.
|
identifiants d'autres bases de données

PE 1: Evidence at protein level;
|
degré de confiance de l'existence (expression) de la protéine


Détails (3)
FT MOD_RES 211 211 Sulfotyrosine (By similarity).
FT DISULFID 87 217
FT DISULFID 105 121
[...]
FT STRAND 111 117
FT HELIX 119 121
|
annotations de la séquence

SQ SEQUENCE 304 AA; 32529 MW; 4C4303C310B7BFFC CRC64;
MCGPDDRCPA RWPGPGRAVK CGKGLAAARP GRVERGGAQR GGAGLELHPL LGGRTWRAAR
DADGCEALGT VAVPFDDDDK IVGGYTCEEN SLPYQVSLNS GSHFCGGSLI SEQWVVSAAH
CYKTRIQVRL GEHNIKVLEG NEQFINAAKI IRHPKYNRDT LDNDIMLIKL SSPAVINARV
STISLPTTPP AAGTECLISG WGNTLSFGAD YPDELKCLDA PVLTQAECKA SYPGKITNSM
FCVGFLEGGK DSCQRDSGGP VVCNGQLQGV VSWGHGCAWK NRPGVYTKVY NYVDWIKDTI
AANS
|
séquence de la protéine

//
|
fin de la fiche


Remarques

extension .txt

également .xml

Python : chaînes de caractères/listes
+ expressions régulières
(+ module xml)


xml
<?xml version='1.0' encoding='UTF-8'?>
<uniprot xmlns="http://uniprot.org/uniprot" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
<entry dataset="Swiss-Prot" created="1994-02-01" modified="2011-01-11" version="111">
<accession>P35030</accession>
<accession>A9Z1Y4</accession>
<accession>P15951</accession>
<accession>Q15665</accession>
[...]
<dbReference type="NCBI Taxonomy" id="9606" key="2"/>
<lineage>
<taxon>Eukaryota</taxon>
<taxon>Metazoa</taxon>
<taxon>Chordata</taxon>
[...]
<feature type="disulfide bond">
<location>
<begin position="228"/>
<end position="242"/>
[...]
<feature type="strand">
<location>
<begin position="133"/>
<end position="137"/>
[...]
<sequence length="304" mass="32529" checksum="4C4303C310B7BFFC" modified="2008-10-14" version="2"
MCGPDDRCPARWPGPGRAVKCGKGLAAARPGRVERGGAQRGGAGLELHPLLGGRTWRAAR
DADGCEALGTVAVPFDDDDKIVGGYTCEENSLPYQVSLNSGSHFCGGSLISEQWVVSAAH
CYKTRIQVRLGEHNIKVLEGNEQFINAAKIIRHPKYNRDTLDNDIMLIKLSSPAVINARV
STISLPTTPPAAGTECLISGWGNTLSFGADYPDELKCLDAPVLTQAECKASYPGKITNSM
FCVGFLEGGKDSCQRDSGGPVVCNGQLQGVVSWGHGCAWKNRPGVYTKVYNYVDWIKDTI
AANS
</sequence>


Menu
1 Rappels

2 Problématique

3 Séquences

4 Structures


6 Conclusion


Protein Data Bank (PDB)

structures : ADN, ARN, protéines, virus...

Rayons-X, RMN, cryo-microscopie électronique


PDB http://www.rcsb.org/pdb/home/home.do

Exemple
HEADER HYDROLASE (SERINE PROTEINASE) 26-OCT-81 2PTN
TITLE ON THE DISORDERED ACTIVATION DOMAIN IN TRYPSINOGEN.
TITLE 2 CHEMICAL LABELLING AND LOW-TEMPERATURE CRYSTALLOGRAPHY
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRYPSIN;
COMPND 3 CHAIN: A;
COMPND 4 EC: 3.4.21.4;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS;
SOURCE 3 ORGANISM_COMMON: CATTLE;
SOURCE 4 ORGANISM_TAXID: 9913
KEYWDS HYDROLASE (SERINE PROTEINASE)
EXPDTA X-RAY DIFFRACTION
[...]
REMARK 2 RESOLUTION. 1.55 ANGSTROMS.
[...]
[...]
ATOM 273 N ALA A 55 6.294 11.611 25.982 1.00 9.30 N
ATOM 274 CA ALA A 55 6.778 12.670 25.099 1.00 9.30 C
ATOM 275 C ALA A 55 7.329 13.864 25.883 1.00 9.30 C
ATOM 276 O ALA A 55 6.747 14.218 26.934 1.00 9.30 O
ATOM 277 CB ALA A 55 5.636 13.154 24.190 1.00 9.30 C
ATOM 278 N ALA A 56 8.461 14.383 25.454 1.00 7.97 N
ATOM 279 CA ALA A 56 9.069 15.522 26.129 1.00 7.97 C
ATOM 280 C ALA A 56 8.143 16.740 26.167 1.00 7.97 C
ATOM 281 O ALA A 56 8.162 17.496 27.169 1.00 7.97 O
ATOM 282 CB ALA A 56 10.414 15.918 25.506 1.00 7.97 C
[...]


PDB

en-tête
——————–
©
coordonnées
©

Coordonnées

PyMOL
Rasmol
VMD
...

Python


Coordonnées
ATOM 601 N LEU A 99 10.007 19.687 17.536 1.00 12.25 N
ATOM 602 CA LEU A 99 9.599 18.429 18.188 1.00 12.25 C
ATOM 603 C LEU A 99 10.565 17.281 17.914 1.00 12.25 C
ATOM 604 O LEU A 99 10.256 16.101 18.215 1.00 12.25 O
ATOM 605 CB LEU A 99 8.149 18.040 17.853 1.00 12.25 C
ATOM 606 CG LEU A 99 7.125 19.029 18.438 1.00 18.18 C
ATOM 607 CD1 LEU A 99 5.695 18.554 18.168 1.00 18.18 C
ATOM 608 CD2 LEU A 99 7.323 19.236 19.952 1.00 18.18 C


Remarques

plusieurs chaînes

plusieurs structures (RMN)

des trous (RX)

Python : chaînes de caractères (tranches) + listes


Plusieurs chaînes

ATOM 955 CD2 TYR A 117 28.547 16.730 59.818 1.00 34.54 C
ATOM 956 CE1 TYR A 117 26.512 14.828 59.696 1.00 34.81 C
ATOM 957 CE2 TYR A 117 28.117 16.089 60.985 1.00 35.96 C
ATOM 958 CZ TYR A 117 27.100 15.139 60.917 1.00 35.42 C
ATOM 959 OH TYR A 117 26.673 14.515 62.069 1.00 37.14 O
ATOM 960 OXT TYR A 117 25.735 19.061 58.351 1.00 32.81 O
TER 961 TYR A 117
ATOM 962 N ARG B 3 42.047 55.053 18.876 1.00 34.90 N
ATOM 963 CA ARG B 3 42.680 56.307 19.383 1.00 35.03 C
ATOM 964 C ARG B 3 43.365 56.041 20.722 1.00 33.56 C
ATOM 965 O ARG B 3 42.720 55.647 21.691 1.00 33.47 O
ATOM 966 CB ARG B 3 41.614 57.395 19.562 1.00 37.48 C
ATOM 967 CG ARG B 3 40.638 57.499 18.394 1.00 41.05 C


Plusieurs structures
MODEL 1
ATOM 1 N GLY A 1 11.935 -10.938 0.352 1.00 0.00 N
ATOM 2 CA GLY A 1 13.344 -10.643 0.600 1.00 0.00 C
ATOM 3 C GLY A 1 13.861 -9.576 -0.330 1.00 0.00 C
ATOM 4 O GLY A 1 14.929 -9.728 -0.931 1.00 0.00 O
[...]
ATOM 934 HB2 GLU A 60 9.981 7.744 1.905 1.00 0.00 H
ATOM 935 HB3 GLU A 60 10.321 6.103 2.451 1.00 0.00 H
ATOM 936 HG2 GLU A 60 12.152 6.972 3.824 1.00 0.00 H
ATOM 937 HG3 GLU A 60 11.700 8.597 3.310 1.00 0.00 H
TER 938 GLU A 60
ENDMDL
MODEL 2
ATOM 1 N GLY A 1 19.334 -6.988 0.864 1.00 0.00 N
ATOM 2 CA GLY A 1 18.296 -6.813 1.874 1.00 0.00 C
ATOM 3 C GLY A 1 18.000 -5.370 2.142 1.00 0.00 C
ATOM 4 O GLY A 1 18.677 -4.724 2.959 1.00 0.00 O
[...]
ATOM 934 HB2 GLU A 60 11.353 9.615 -0.439 1.00 0.00 H
ATOM 935 HB3 GLU A 60 13.095 9.643 -0.204 1.00 0.00 H
ATOM 936 HG2 GLU A 60 13.380 10.930 -2.203 1.00 0.00 H
ATOM 937 HG3 GLU A 60 11.654 10.817 -2.534 1.00 0.00 H
TER 938 GLU A 60
ENDMDL


Des trous
[...]
ATOM 7568 CB LYS B 72 -59.462-109.221 -72.440 1.00 31.64 C
ATOM 7569 CG LYS B 72 -58.524-109.915 -73.424 1.00 31.85 C
ATOM 7570 CD LYS B 72 -58.889-109.602 -74.868 1.00 32.02 C
ATOM 7571 CE LYS B 72 -58.174-110.533 -75.837 1.00 31.61 C
ATOM 7572 NZ LYS B 72 -58.629-110.335 -77.242 1.00 31.27 N
ATOM 7573 N GLY B 73 -61.309-106.416 -72.158 1.00 31.85 N
ATOM 7574 CA GLY B 73 -62.485-105.832 -71.510 1.00 30.84 C
ATOM 7575 C GLY B 73 -63.598-106.848 -71.303 1.00 29.65 C
ATOM 7576 O GLY B 73 -64.660-106.750 -71.920 1.00 28.85 O
ATOM 7577 N SER B 74 -63.354-107.820 -70.425 1.00 28.53 N
ATOM 7578 CA SER B 74 -64.301-108.911 -70.179 1.00 27.75 C
ATOM 7579 C SER B 74 -64.180-109.438 -68.754 1.00 26.72 C
ATOM 7580 O SER B 74 -65.113-110.041 -68.227 1.00 24.48 O
ATOM 7581 CB SER B 74 -64.070-110.058 -71.166 1.00 26.32 C
ATOM 7582 OG SER B 74 -64.505-109.716 -72.470 1.00 25.54 O
ATOM 7583 N GLN B 79 -62.682-105.888 -62.336 1.00 42.85 N
ATOM 7584 CA GLN B 79 -63.246-104.902 -63.248 1.00 42.57 C
ATOM 7585 C GLN B 79 -62.146-104.278 -64.103 1.00 42.60 C
ATOM 7586 O GLN B 79 -60.992-104.191 -63.681 1.00 42.45 O
ATOM 7587 CB GLN B 79 -63.996-103.819 -62.464 1.00 42.46 C
ATOM 7588 CG GLN B 79 -64.950-102.964 -63.300 1.00 42.30 C
ATOM 7589 CD GLN B 79 -66.093-103.764 -63.905 1.00 42.15 C
ATOM 7590 OE1 GLN B 79 -66.388-104.879 -63.472 1.00 42.18 O
ATOM 7591 NE2 GLN B 79 -66.743-103.194 -64.911 1.00 41.70 N
ATOM 7592 N VAL B 80 -62.514-103.846 -65.305 1.00 42.30 N
ATOM 7593 CA VAL B 80 -61.549-103.342 -66.275 1.00 42.03 C
ATOM 7594 C VAL B 80 -60.882-102.055 -65.796 1.00 42.42 C
ATOM 7595 O VAL B 80 -61.544-101.165 -65.260 1.00 43.09 O
[...]


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4 Structures


6 Conclusion


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GenBank Z71230
LOCUS Z71230 124 bp DNA linear PLN 14-NOV-2006
DEFINITION Nicotiana tabacum chloroplast JLA region, sequence 2.
ACCESSION Z71230
VERSION Z71230.1 GI:1279604
KEYWORDS rpl2 gene; transfer RNA-His; trnH gene.
SOURCE chloroplast Nicotiana tabacum (common tobacco)
ORGANISM Nicotiana tabacum
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
asterids; lamiids; Solanales; Solanaceae; Nicotianoideae;
Nicotianeae; Nicotiana.
AUTHORS Goulding,S.E., Olmstead,R.G., Morden,C.W. and Wolfe,K.H.
TITLE Ebb and flow of the chloroplast inverted repeat
JOURNAL Mol. Gen. Genet. 252 (1-2), 195-206 (1996)
PUBMED 8804393
[...]
source 1..124
/organism="Nicotiana tabacum"
/organelle="plastid:chloroplast"
/mol_type="genomic DNA"
/isolate="Cuban cahibo cigar, gift from President Fidel
Castro"
gene <1..11
/gene="rpl2"


GenBank NC_001610
LOCUS NC_001610 17084 bp DNA circular MAM 14-APR-2009
DEFINITION Didelphis virginiana mitochondrion, complete genome.
ACCESSION NC_001610
VERSION NC_001610.1 GI:5835037
DBLINK Project: 11806
KEYWORDS .
SOURCE mitochondrion Didelphis virginiana (North American opossum)
ORGANISM Didelphis virginiana
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Metatheria; Didelphimorphia; Didelphidae; Didelphis.
AUTHORS Janke,A., Feldmaier-Fuchs,G., Thomas,W.K., von Haeseler,A. and
Paabo,S.
TITLE The marsupial mitochondrial genome and the evolution of placental
mammals
JOURNAL Genetics 137 (1), 243-256 (1994)
PUBMED 8056314
[...]
source 1..17084
/organism="Didelphis virginiana"
/organelle="mitochondrion"
/mol_type="genomic DNA"
/isolate="fresh road killed individual"
/tissue_type="liver"
/dev_stage="adult"


GenBank 252544
LOCUS 252544 649 bp RNA linear VRL 19-SEP-2002
DEFINITION gene 7 3' end, 5' end, segment 7 [human rotavirus, strain Wa,
Genomic RNA, 425 nt 2 segments].
ACCESSION
VERSION GI:252544
KEYWORDS .
SOURCE Human rotavirus A
ORGANISM Human rotavirus A
Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Rotavirus;
Rotavirus A.
[...]
source 1..649
/organism="Human rotavirus A"
/mol_type="genomic RNA"
/strain="Wa"
ORIGIN
1 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
601 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnn
//


PDB 7GBP, chaîne D, res 67

PP Université Paris Diderot - Paris 7
Oups !
58

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6 Conclusion


TTGTCACCTGTACACTGGCATTACTACACAGAAACCCAGATGTCCGTTACC
AAGATGACCGTGTGTCATTCATTCCTAAGATTCAAAATGATTTCGATGGCA
TTGATCCTGAACTGTTTGAATTGAGAAAAGCTGTTATGGACACCAATGAAA
données : séquences, structures...
AAAAAATGTTCCGTGACGACACTTTCGGCAAGAACCTGAATGCAAACACAA
GACTCTTTGATGATGAGACTAGTTCATCCTCTTTTAAGCAAAATTCCTCTC
CCTCGGAAGTAACGGAGCAACCTGTGCAACCAACCTCCGCTGTCATGGGTA
GCTTCTTGTCTCCACAGTACCAACGTGCGTCATCTGCTTCTCGTACTAATC
ATAATACAAGCACCTCCAGTTTAATGAAGCCTGAATCAAGTCTCTACCTGG
ATAAATCATATTCGCATTTTAACAACAACGGCAGCAACGAAAACGCCCGCA
CATATTTGTAATCCAATATATACTCACATGTAACAACTTATTATATAAATA
AAGGATATCCTACATTATATTTCATAGAAAACCGCTCAAAAAGGTGTATTA
CATCCCAACACCACACATATTTCAGCGATAAAAACCTTAAATGTGAAATTC
CTGCTTCCTTAAATGTACGCAATTGCCGCTTTTTTCTGACATCTTTTTTGA
AAGGAAACAGATCCTCCAGAAGGGATTTACTGTTGGCTATTTTGTGTTAGA
ATAATAGATTAGGTTGCGTAAGTCATGGTCGAAAATAGTACGCAGAAGGCC
GGAAATGATGATAATAGCTCTACCAAGCCATATTCGGAGGCGTTTTTCTTA
AACCCAACGCCTGGATTAGAAGCTGAGCACTCAAGCACATCGCCTGCCCCC
AACTTGAAAATCGGTATGCTATTATCAATGCTTTACAATTCTGTCGGTTAC
GAGGATCATTGCCCTCAAGGTGGCGAATATTCGGATTTATTGAGAAATTTG
TGTGAAGCTATTTTGCCATCTTACGAAATTATTGAACGCTACAAGAACCAC

il existe des normes

... pas toujours respectées

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3 Séquences

4 Structures


6 Conclusion


Références
Cours de J.-C. Gelly Bases de données en biologie

Bioinformatics for dummies de J.-M. Claverie et C. Notredame

BioStar
Incorrect / unusual entries in main databases (GenBank, UniProt, PDB) ?
http://biostar.stackexchange.com/questions/10869/
incorrect-unusual-entries-in-main-databases-genbank-uniprot-pdb


Références (2)
format FASTA – http://en.wikipedia.org/wiki/FASTA_format

GenBank – http://www.ncbi.nlm.nih.gov/
format :
http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html

UniProt – http://www.uniprot.org/
format : http://www.uniprot.org/manual/

PDB – http://www.rcsb.org/pdb/home/home.do
format :
http://www.wwpdb.org/documentation/format23/v2.3.html


Crédits graphiques
Squidonius (Wikimedia)

Ralphbijker (Flickr)

USDA/ARS
Viktorvoigt (Wikimedia)
Icons-Land (Findicons)

herzogbr (Flickr)

Icons-Land (Findicons)

PAPYRARRI (Flickr)


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