Benutzer:Easelpeasel/B/Liste von Tools
Todo
Datenbanken
GeneSpring GX Sammlung
von Agilent Technologies (agilent)
Der SWISS-MODEL-Server des SWISS Institut of Bioinformatics in Lausanne
Docking-Beispiel mit GOLD
Pharmakophor-Modelle
BLAT
SAM-/BAM-Format
Parasitic Nematode Sequencing Project
EST-Datenbank (z. B. dbEST oder TIGR Gene Indices)
ProtEST
HomoloGene
Molecular Biology Open Software Suite (EMBOSS; Rice et al. 2000)
Expasy
EMBnet
fasta
fastq
BWA
Bowtie
SNP-o-matic
NextGenMap
GCG-Wisconsin-Package (Biova)
DNA-Star-Software (DNASTAR Inc.)
Vector-NTI-Software
Glimmer
Genscan
https://en.wikipedia.org/wiki/Models_of_DNA_evolution
European Nucleotide Archive
DNA Database of Japan
BLAST-Algorithmus (ncbi-blast, embl-blast, ddbj-blast)
Wisconsin Suite (GCG)
GeneQuiz
FAST-Algorithmus
Silicon Graphics Octane 2 MOLCAD/Sybyl (Tripos Inc.)
Brookhaven Protein Data Bank (PDB)
bioSCOUT
Sequence Retrieval System (SRS)
BioWisdom
Genomes OnLine Database Gold (http://www.genomesonline.org/)
Swiss-Prot
TrEMBL
PIR-PSD
IntelliGenetics Suite
PROSITE
PRINTS
Pfam
Interpro
OnlineMendelian-Inheritance-in-Man(OMIM)-Datenbank
dbGaP
Online-Mendelian-Inheritance-in-Animals(OMIA)-Datenbank
Mouse Genome Database (MGD)
FlyBase
WormBase
Datenbank Structural Classification of Proteins 2
PhenomicDB
https://en.wikipedia.org/wiki/CATH_database
PROSITE
PRINTS
Pfam
Interpro
OnlineMendelian-Inheritance-in-Man(OMIM)-Datenbank
dbGaP
Online-Mendelian-Inheritance-in-Animals(OMIA)-Datenbank
Mouse Genome Database (MGD)
FlyBase
WormBase
Datenbank Structural Classification of Proteins 2
PhenomicDB
https://en.wikipedia.org/wiki/CATH_database
PROCHECK
Oracle
MS-Access
Informax
DB2
MySQL
GenBank
Entrez
Human Genome Variation Database (gwas)
GWAS Central
CAP3 (cap)
Phrap (phrap)
UniGene
stackPACK (stackpack).
Chimera. https://www.cgl.ucsf.edu/chimera/. Zugegriffen: 04.10.2017
DOCK. http://dock.compbio.ucsf.edu/. Zugegriffen: 04.10.2017
FlexX. https://www.biosolveit.de/FlexX/. Zugegriffen: 04.10.2017
GOLD. https://www.ccdc.cam.ac.uk/solutions/csd-discovery/components/gold/. Zugegriffen: 04.10.2017
Ligandscout. http://www.inteligand.com/ligandscout/. Zugegriffen: 04.10.2017
MOE. https://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm. Zugegriffen: 04.10.2017
PDB. http://www.rcsb.org/. Zugegriffen: 04.10.2017
Phase. https://www.schrodinger.com/phase. Zugegriffen: 04.10.2017
SignalP. http://www.cbs.dtu.dk/services/SignalP/. Zugegriffen: 04.10.2017
Spdbv. http://www.expasy.org/spdbv/. Zugegriffen: 04.10.2017
SWISS-MODEL. https://swissmodel.expasy.org/. Zugegriffen: 04.10.2017
TMHMM. http://www.cbs.dtu.dk/services/TMHMM/. Zugegriffen: 04.10.2017
ArrayExpress des EBI (arrayexpress).
Bioconductor
(bioconductor), TM4 (tm4) oder GenePattern (genepattern).
Gene Expression Omnibus (geo)
agilent. http://www.genomics.agilent.com. Zugegriffen: 04.10.2017
affymetrix. http://www.affymetrix.com/. Zugegriffen: 04.10.2017
arrayexpress. http://www.ebi.ac.uk/arrayexpress/index.html. Zugegriffen: 04.10.2017
bioconductor. https://www.bioconductor.org/. Zugegriffen: 04.10.2017
biomodels. https://www.ebi.ac.uk/biomodels-main/. Zugegriffen: 04.10.2017
ecell. http://www.e-cell.org. Zugegriffen: 04.10.2017
ercc. http://jimb.stanford.edu/ercc/. Zugegriffen: 04.10.2017
geo. https://www.ncbi.nlm.nih.gov/geo/. Zugegriffen: 04.10.2017
genedisruptionproject. http://www.fruitfly.org/p_disrupt/index.html. Zugegriffen: 04.10.2017
genepattern. http://software.broadinstitute.org/cancer/software/genepattern/. Zugegriffen: 04.10.2017
hgvdb. http://www.hgvd.genome.med.kyoto-u.ac.jp/. Zugegriffen: 04.10.2017
hmdb. http://www.hmdb.ca/. Zugegriffen: 04.10.2017
hpp. http://www.thehpp.org/. Zugegriffen: 04.10.2017
intact. http://www.ebi.ac.uk/intact/. Zugegriffen: 04.10.2017
maqc. http://www.fda.gov/ScienceResearch/BioinformaticsTools/MicroarrayQualityControlProject/default.htm.
Zugegriffen: 04.10.2017
melanie. http://world-2dpage.expasy.org/melanie/. Zugegriffen: 04.10.2017
miame. http://fged.org/projects/miame/. Zugegriffen: 04.10.2017
sage. http://www.sagenet.org/. Zugegriffen: 04.10.2017
sagemap. https://www.ncbi.nlm.nih.gov/projects/SAGE/. Zugegriffen: 04.10.2017
sensigent. http://www.sensigent.com/products/cyranose.html. Zugegriffen: 04.10.2017
string. http://string-db.org/. Zugegriffen: 04.10.2017
tm4. http://www.tm4.org/. Zugegriffen: 04.10.2017
Protein Information Resource (PIR)
BioJava
Circos
https://en.wikipedia.org/wiki/List_of_open-source_bioinformatics_software
https://en.wikipedia.org/wiki/List_of_biological_databases
https://en.wikipedia.org/wiki/List_of_biological_databases
cap. http://doua.prabi.fr/software/cap3. Zugegriffen: 20.09.2017
dbest. https://www.ncbi.nlm.nih.gov/dbEST/. Zugegriffen: 20.09.2017
dbgss. https://www.ncbi.nlm.nih.gov/dbGSS/. Zugegriffen: 20.09.2017
dbsnp. https://www.ncbi.nlm.nih.gov/SNP/. Zugegriffen: 20.09.2017
dbsts. https://www.ncbi.nlm.nih.gov/dbSTS/. Zugegriffen: 20.09.2017
ebi-gwas. http://www.ebi.ac.uk/gwas/. Zugegriffen: 20.09.2017
grailexp. http://compbio.ornl.gov/grailexp/. Zugegriffen: 20.09.2017
gwas. http://pbil.univ-lyon1.fr/members/duret/cours/insa2004/exercise4/pgrail.html. Zugegriffen: 20.09.2017
helix-nebula. http://www.helix-nebula.eu/usecases/embl-use-case. Zugegriffen: 20.09.2017
homologene. http://www.ncbi.nlm.nih.gov/homologene/. Zugegriffen: 20.09.2017
hts-mapper. http://www.ebi.ac.uk/~nf/hts_mappers/. Zugegriffen: 20.09.2017
humatrix. https://www.humatrix.de/. Zugegriffen: 20.09.2017
image. http://imageconsortium.org/. Zugegriffen: 03.01.2017
nematode. http://www.nematode.net/. Zugegriffen: 20.09.2017
ngs-knowledge-base. https://goo.gl/HIaY1W. Zugegriffen: 20.09.2017
ngs-movie. https://www.youtube.com/watch?v=jFCD8Q6qSTM. Zugegriffen: 20.09.2017
nhgri-gwas. https://www.genome.gov/20019523/. Zugegriffen: 20.09.2017
nih-biowolf. https://hpc.nih.gov/. Zugegriffen: 20.09.2017
pahdb. http://www.pahdb.mcgill.ca/. Zugegriffen: 20.09.2017
phrap. http://www.phrap.org/. Zugegriffen: 20.09.2017
pyrosequencing. http://www.pyrosequencing.com/. Zugegriffen: 20.09.2017
sam-tools. https://en.wikipedia.org/wiki/SAMtools. Zugegriffen: 20.09.2017
stackpack. http://genoma.unsam.edu.ar/stackpack.old/index.html. Zugegriffen: 03.01.2017
stratipharm. http://www.stratipharm.de/. Zugegriffen: 20.09.2017
unigene. http://www.ncbi.nlm.nih.gov/UniGene/. Zugegriffen: 20.09.2017
vfa-personalisiert. http://www.vfa.de/personalisiert/. Zugegriffen: 20.09.2017
wikibook-ngs. https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29. Zugegriffen: 20.09.2017
cap. http://doua.prabi.fr/software/cap3. Zugegriffen: 20.09.2017
dbest. https://www.ncbi.nlm.nih.gov/dbEST/. Zugegriffen: 20.09.2017
dbgss. https://www.ncbi.nlm.nih.gov/dbGSS/. Zugegriffen: 20.09.2017
dbsnp. https://www.ncbi.nlm.nih.gov/SNP/. Zugegriffen: 20.09.2017
dbsts. https://www.ncbi.nlm.nih.gov/dbSTS/. Zugegriffen: 20.09.2017
ebi-gwas. http://www.ebi.ac.uk/gwas/. Zugegriffen: 20.09.2017
grailexp. http://compbio.ornl.gov/grailexp/. Zugegriffen: 20.09.2017
gwas. http://pbil.univ-lyon1.fr/members/duret/cours/insa2004/exercise4/pgrail.html. Zugegriffen: 20.09.2017
helix-nebula. http://www.helix-nebula.eu/usecases/embl-use-case. Zugegriffen: 20.09.2017
homologene. http://www.ncbi.nlm.nih.gov/homologene/. Zugegriffen: 20.09.2017
hts-mapper. http://www.ebi.ac.uk/~nf/hts_mappers/. Zugegriffen: 20.09.2017
humatrix. https://www.humatrix.de/. Zugegriffen: 20.09.2017
image. http://imageconsortium.org/. Zugegriffen: 03.01.2017
nematode. http://www.nematode.net/. Zugegriffen: 20.09.2017
ngs-knowledge-base. https://goo.gl/HIaY1W. Zugegriffen: 20.09.2017
ngs-movie. https://www.youtube.com/watch?v=jFCD8Q6qSTM. Zugegriffen: 20.09.2017
nhgri-gwas. https://www.genome.gov/20019523/. Zugegriffen: 20.09.2017
nih-biowolf. https://hpc.nih.gov/. Zugegriffen: 20.09.2017
pahdb. http://www.pahdb.mcgill.ca/. Zugegriffen: 20.09.2017
phrap. http://www.phrap.org/. Zugegriffen: 20.09.2017
pyrosequencing. http://www.pyrosequencing.com/. Zugegriffen: 20.09.2017
sam-tools. https://en.wikipedia.org/wiki/SAMtools. Zugegriffen: 20.09.2017
stackpack. http://genoma.unsam.edu.ar/stackpack.old/index.html. Zugegriffen: 03.01.2017
stratipharm. http://www.stratipharm.de/. Zugegriffen: 20.09.2017
unigene. http://www.ncbi.nlm.nih.gov/UniGene/. Zugegriffen: 20.09.2017
vfa-personalisiert. http://www.vfa.de/personalisiert/. Zugegriffen: 20.09.2017
wikibook-ngs. https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29. Zugegriffen: 20.09.2017
bioedit. http://www.mbio.ncsu.edu/bioedit/bioedit.html. Zugegriffen: 01.10.2017
blast. https://blast.ncbi.nlm.nih.gov. Zugegriffen: 01.10.2017
clustalomega. https://www.ebi.ac.uk/Tools/msa/clustalo/. Zugegriffen: 01.10.2017
ddbj-blast. http://ddbj.nig.ac.jp/blast/blastn?lang=en. Zugegriffen: 01.10.2017
embnet. http://www.embnet.org/. Zugegriffen: 01.10.2017
embl-blast. https://www.ebi.ac.uk/Tools/sss/ncbiblast/nucleotide.html. Zugegriffen: 01.10.2017
emboss. http://emboss.sourceforge.net/. Zugegriffen: 01.10.2017
expasy. https://www.expasy.org/. Zugegriffen: 01.10.2017
genscan. http://genes.mit.edu/GENSCAN.html. Zugegriffen: 01.10.2017
glimmer. http://ccb.jhu.edu/software/glimmer/index.shtml. Zugegriffen: 01.10.2017
ncbi. http://www.ncbi.nlm.nih.gov/. Zugegriffen: 01.10.2017
ncbi-blast. http://www.ncbi.nlm.nih.gov/blast/. Zugegriffen: 01.10.2017
sanger. http://www.sanger.ac.uk/. Zugegriffen: 01.10.2017
seaview. http://doua.prabi.fr/software/seaview. Zugegriffen: 01.10.2017
treeview. http://etetoolkit.org/treeview/. Zugegriffen: 01.10.2017
| Name | Link | Beschreibung | Veröffentlichung | Letztes Update | Typ | Entwickler |
|---|---|---|---|---|---|---|
| streptomedb | ||||||
| streptdb | ||||||
| methdb | ||||||
| https://cbs.umn.edu/cgc/home | ||||||
| bankit | http://www.ncbi.nlm.nih.gov/WebSub/?tool=genbank | |||||
| cath | http://www.cathdb.info/ | |||||
| dbgap | http://www.ncbi.nlm.nih.gov/gap | |||||
| ddbj | http://www.ddbj.nig.ac.jp/ | |||||
| ebi | http://www.ebi.ac.uk/
http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html |
|||||
| ena | http://www.ebi.ac.uk/ena/ | |||||
| entrez | http://www.ncbi.nlm.nih.gov/nucleotide
https://www.ncbi.nlm.nih.gov/books/NBK3836/ |
|||||
| expasy | http://www.expasy.org/ | |||||
| flybase | http://www.flybase.org/ | |||||
| gb-sample | http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html | |||||
| genbank | http://www.ncbi.nlm.nih.gov/Genbank/ | |||||
| homologene | http://www.ncbi.nlm.nih.gov/homologene | |||||
| interpro | http://www.ebi.ac.uk/interpro/ | |||||
| mgd | http://www.informatics.jax.org/ | |||||
| nar | http://nar.oxfordjournals.org/ | |||||
| ncbi | http://www.ncbi.nlm.nih.gov/ | |||||
| nig | https://www.nig.ac.jp/nig/ | |||||
| omia | http://omia.angis.org.au/home/ | |||||
| omim | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM | |||||
| pdb | http://www.rcsb.org/pdb/home/home.do | |||||
| pdb-models | http://www.rcsb.org/pdb/search/searchModels.do | |||||
| pfam | http://pfam.xfam.org/ | |||||
| phenomicdb | http://www.phenomicdb.de/ | |||||
| pir | http://pir.georgetown.edu/pirwww/dbinfo/pir_psd.shtml | |||||
| prints | http://bioinf.man.ac.uk/dbbrowser/PRINTS/ | |||||
| prosite | http://prosite.expasy.org/ | |||||
| prosite-manual | http://prosite.expasy.org/prosuser.html | |||||
| pubchem | http://pubchem.ncbi.nlm.nih.gov/ | |||||
| scop | http://scop.mrc-lmb.cam.ac.uk/scop/ | |||||
| Structural Classification of Proteins 2 scop2 [1] | http://scop2.mrc-lmb.cam.ac.uk/ | The main focus of SCOP2 is on knowledge-based expert analysis and classification of proteins that are structurally characterized and deposited in the Protein Data Bank, PDB. Proteins are organized according to their structural and evolutionary relationships, but, in contrast to SCOP, instead of a simple tree-like hierarchy these relationships form a complex network of nodes. The classification of proteins is described in terms of a directed acyclic graph in which each node defines a relationship of particular type and is exemplified by a region of protein structure and sequence. Importantly, there can be more than one parental node for a child node that allows multiple routes to a particular relationship. | MRC Laboratory of Molecular Biology | |||
| Sequin--A DNA Sequence Submission Tool | https://www.ncbi.nlm.nih.gov/Sequin/ | Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database. It is capable of handling simple submissions that contain a single short mRNA sequence, and complex submissions containing long sequences, multiple annotations, gapped sequences, or phylogenetic and population studies. A single Sequin file should contain less than 10,000 sequences for maximum performance. Larger submissions should be made with tbl2asn . | ||||
| swissprot UniProtKB/Swiss-Prot | nicht ganz klar wo der Unterschied zum unteren ist | UniProtKB/Swiss-Prot is the manually annotated and reviewed section of the UniProt Knowledgebase (UniProtKB).
It is a high quality annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions. |
||||
| The TIGR Maize Database | http://maize.jcvi.org/ | to evaluate two gene-enrichment techniques, methylation filtration and high Cot selection, to sequence the maize 'genespace'. Draft assemblies of 287 maize BAC clones selected by the maize community and the Consortium were also produced in the Consortium project.
We have recently developed an improved version of the TIGR annotation pipeline optimized for maize genomic assemblies. The latest maize genomic assemblies obtained by gene-enrichment (AZM5) and the 287 maize draft BAC assemblies have been annotated using the improved pipeline. Gene model annotation and functional annotation can be accessed via the TIGR maize BLAST server or the TIGR maize gbrowse display. |
19.3.2017 | Datenbank | J. Craig Venter Institute | |
| uniprot [2] | The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. | Kontinuierlich | Datenbank | UniProt consortium members EMBL SIB Swiss Institute of Bioinformatics Protein Information Resource (PIR) | ||
| Wormbase [3] | http://www.wormbase.org/ | WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes. Founded in 2000, the WormBase Consortium is led by Paul Sternberg of CalTech, Paul Kersey of the EBI, Matt Berriman of the Wellcome Trust Sanger Institute, and Lincoln Stein of the Ontario Institute for Cancer Research. | Kontinuierlich | Datenbank | Founded in 2000, the WormBase Consortium is led by Paul Sternberg of CalTech, Paul Kersey of the EBI, Matt Berriman of the Wellcome Trust Sanger Institute, and Lincoln Stein of the Ontario Institute for Cancer Research. | |
| Worldwide Protein Data Bank (wwpdb) [4] | http://www.wwpdb.org/ | 3D structures of proteins, nucleic acids and complex assemblies | Kontinuierlich | Datenbank | Worldwide Protein Data Bank Foundation [1] |
Software
https://en.wikipedia.org/wiki/List_of_open-source_bioinformatics_software
https://en.wikipedia.org/wiki/BioJava
| Name | Beschreibung | Veröffentlichung | Letztes Update | Typ | Lizenz | Entwickler |
|---|---|---|---|---|---|---|
- ↑ Antonina Andreeva, Dave Howorth, Cyrus Chothia, Eugene Kulesha, Alexey G. Murzin: SCOP2 prototype: a new approach to protein structure mining. In: Nucleic Acids Research. Band 42, D1, 1. Januar 2014, ISSN 0305-1048, S. D310–D314, doi:10.1093/nar/gkt1242 (oup.com [abgerufen am 23. Februar 2018]).
- ↑ The UniProt Consortium: UniProt: the universal protein knowledgebase. In: Nucleic Acids Research. Band 45, D1, 4. Januar 2017, ISSN 0305-1048, S. D158–D169, doi:10.1093/nar/gkw1099 (doi.org [abgerufen am 23. Februar 2018]).
- ↑ Raymond Y N Lee, Raymond Y N Lee, Kevin L Howe, Todd W Harris, Valerio Arnaboldi: WormBase 2017: molting into a new stage. In: Nucleic Acids Research. Band 46, D1, 4. Januar 2018, ISSN 0305-1048, S. D869–D874, doi:10.1093/nar/gkx998 (doi.org [abgerufen am 23. Februar 2018]).
- ↑ Helen Berman, Kim Henrick, Haruki Nakamura: Announcing the worldwide Protein Data Bank. In: Nature Structural & Molecular Biology. Band 10, Nr. 12, 2003/12, ISSN 1545-9985, S. 980–980, doi:10.1038/nsb1203-980 (nature.com [abgerufen am 23. Februar 2018]).
