Biyoinformatik Veri Tabanlarını ve Yazılımlarını detaylı olarak listeleme çalışmalarını yapmaktayız. URL adresleri üzerinden kolaylıkla istediğiniz veri tabanına ve yazılıma ulaşabilirsiniz. Liste sürekli güncellenecektir ve açıklamalar da eklenecektir.
| Veri Tabanları ve Yazılımlar | URL | Açıklama |
|---|---|---|
| Kitaplar | ||
| Essentials of Bioinformatics Volume I | ||
| Essentials of Bioinformatics Volume II | ||
| Essentials of Bioinformatics Volume III | ||
| Bioinformatics A Student’s Companion | ||
| Bioinformatics for Beginners | ||
| Gene Cloning and DNA Analysis: An Introduction | ||
| Bioinformatics and the Cell | ||
| Introduction to Biotechnology | ||
| Bioinformatics Data Skills | ||
| Introduction to Bioinformatics | ||
| DİZİ KAYNAKLARI | ||
| NCBI | http://www.ncbi.nlm.nih.gov/ | |
| EBI | https://www.ebi.ac.uk/ | |
| UniProt | http://www.uniprot.org/ | |
| GenBank | https://www.ncbi.nlm.nih.gov/ | |
| EMBL | http://www.embl.org/ | |
| DNA data Bank of Japan | http://www.ddbj.nig.ac.jp/ | |
| Ensembl | https://www.ensembl.org/index.html | |
| GeneCards | genecards.org | |
| Nucleic acid database | http://ndbserver.rutgers.edu/ | |
| DNA | ||
| Allele Frequency Net Database | allelefrequencies.net | |
| Database of single nucleotide polymorphisms | ncbi.nlm.nih.gov/snp | |
| Database of essential genes | essentialgene.org | |
| European Genome-phenome Archive | https://www.ebi.ac.uk/ega/home | |
| EUGene | eugenes.org | |
| JASPAR | http://jaspar.genereg.net/ | |
| Japanese Genotype-phenotype Archive | trace.ddbj.nig.ac.jp/jga | |
| NCBI Reference Sequence Database | ncbi.nlm.nih.gov/refseq | |
| PolymiRTS | compbio.uthsc.edu/miRSNP | |
| 1000 Genomes | 1000genomes.org | |
| UCSC Genome Browser | https://genome.ucsc.edu/ | |
| The Eukaryotic Promoter Database (EPD) | https://epd.epfl.ch//index.php | |
| TRANSFAC | http://genexplain.com/transfac/ | |
| ENCODE | https://www.encodeproject.org | |
| HapMap | https://ftp.ncbi.nlm.nih.gov/hapmap/ | |
| Array Express | https://www.ebi.ac.uk/arrayexpress/ | |
| The Human Gene Mutation Database | http://www.hgmd.cf.ac.uk/ac/index.php | |
| The Personal Genome Project | https://www.personalgenomes.org/ | |
| SNPedia | https://snpedia.com/ | |
| ExoCarta | http://www.exocarta.org/ | |
| CAP3 | http://doua.prabi.fr/software/cap3 | |
| Staden paketi—Gap4/Gap5 | http://sourceforge.net/projects/staden | |
| Phrap | http://www.phrap.org/phredphrapconsed.html#block_ phrap | |
| VERİ TABANI ARAMA | ||
| 2013 NAR Veri tabanlarının alfabetik listesi | http://www.oxfordjournals.org/nar/database/a/ | |
| NCBI BLAST | http://blast.ncbi.nlm.nih.gov/ | |
| NCBI BLAST+ (EBI) | http://www.ebi.ac.uk/Tools/sss/ncbiblast/nucleotide.html | |
| UniProt BLAST | http://www.uniprot.org/blast/ | |
| Dot Plot ANALİZİ | ||
| Dotlet | http://myhits.isb-sib.ch/cgi-bin/dotlet | |
| Jdotter | http://athena.bioc.uvic.ca/virology-ca-tools/jdotter/ | |
| YASS | http://bioinfo.lifl.fr/yass/yass.php | |
| İKİLİ HİZALAMA | ||
| BLAST2Seq | http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE= BlastSearch&PROG_DEF=blastn&BLAST_PROG_ DEF=megaBlast&BLAST_SPEC=blast2seq | |
| EBI | http://www.ebi.ac.uk/Tools/psa/ | |
| LALIGN | http://www.ch.embnet.org/software/LALIGN_form.html | |
| ÇOKLU DİZİ HİZALAMA (MSA) | ||
| EBI | http://www.ebi.ac.uk/Tools/msa/ | |
| PRALINE | http://www.ibi.vu.nl/programs/pralinewww/ | |
| MUSCLE | http://www.ebi.ac.uk/Tools/msa/muscle/ | |
| MAFFT | http://www.ebi.ac.uk/Tools/msa/mafft/ | |
| GGSEARCH | http://nebc.nox.ac.uk/bioinformatics/docs/ggsearch.html | |
| HMMER | http://hmmer.org/ | |
| G-PAS | http://www.mybiosoftware.com/g-pas-2-0-fast-gpu-vesion-pairwise-alignment-algorithms.html | |
| EMBOSS Needle | https://www.ebi.ac.uk/Tools/psa/emboss_needle/ | |
| NW-align | https://zhanglab.ccmb.med.umich.edu/NW-align/ | |
| MUMmer | http://mummer.sourceforge.net/ | |
| MCALIGN2 | http://www.homepages.ed.ac.uk/pkeightl//mcalign/mcinstructions.html | |
| NW-align | http://www.bioinf.org.uk/software/nw/ | |
| STRETCHER | https://galaxy.pasteur.fr/?form=stretcher | |
| Matcher | https://www.ebi.ac.uk/Tools/psa/emboss_matcher/ | |
| SAM | https://web.archive.org/web/20080509161215/http://www.cse.ucsc.edu/ research/compbio/sam.html | |
| SWIMM | https://github.com/enzorucci/SWIMM | |
| ALLALIGN | http://www.allalign.com/ | |
| SWIPE | https://dna.uio.no/swipe/ | |
| MSA GÖRÜNTÜLEME | ||
| Boxshade | https://embnet.vital-it.ch/software/BOX_form.html | |
| ESPript | http://espript.ibcp.fr/ESPript/ESPript/ | |
| Expasy | http://www.expasy.org/. | |
| DNA MARKER ANALİZİ | ||
| Ntedit | https://github.com/bcgsc/ntEdit | |
| NTSYSpc | http://www.appliedbiostat.com/ntsyspc/ntsyspc.html | |
| DARwin 5 | https://darwin.cirad.fr/index.php | |
| PowerMarker | https://brcwebportal.cos.ncsu.edu/powermarker/ | |
| FİLOGENETİK ANALİZ | ||
| MEGA | http://www.megasoftware.net | |
| PYHLIP | http://evolution.gs.washington.edu/phylip.html | |
| PAUP | https://paup.phylosolutions.com/ | |
| Filogenetik analiz yazılımları koleksiyonu | http://evolution.genetics.washington.edu/phylip/software. html#methods | |
| TreeFam | treefam.org | |
| NGPhylogenyFR | https://ngphylogeny.fr/ | |
| PRİMER TASARIMI | ||
| PRIMER3 | frodo.wi.mit.edu/ | |
| Gene Fisher | http://bibiserv.techfak.uni-bielefeld.de/genefisher/ | |
| Web Primer | https://www.yeastgenome.org/cgi-bin/web-primer?name=YML058W | |
| PCR Designer | http://cedar.genetics.soton.ac.uk/public_html/primer.html | |
| Primo Pro 3.4 | http://www.changbioscience.com/primo/primo.html | |
| EPRIMER3 | http://bioinfo.nhri.org.tw/cgi-bin/emboss/eprimer3 | |
| PrimerQuest | https://eu.idtdna.com/Primerquest/Home/Index | |
| MethPrimer | http://www.urogene.org/methprimer/ | |
| MEDUSA | http://combo.dbe.unifi.it/medusa | |
| Eurofins genomics | https://www.eurofinsgenomics.eu/en/dna-rna-oligonucleotides/oligo-tools/primer-design-tools/ | |
| Primer plus3 | http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi | |
| Genscript | https://www.genscript.com/tools/pcr-primers-designer | |
| BiSearch | http://bisearch.enzim.hu/?m=genompsearch | |
| Primer-BLAST | https://www.ncbi.nlm.nih.gov/tools/primer-blast/ | |
| Primer design-M | https://www.hiv.lanl.gov/content/sequence/PRIMER_DESIGN/primer_ design.html | |
| Primer Designer Tool | https://www.thermofisher.com/tr/en/home/life-science/sequencing/sanger-sequencing/pre-designed-primers-pcr-sanger-sequencing.html | |
| MFEprimer | http://mfeprimer.igenetech.com | |
| Primer4 clades | http://maya.ccg.unam.mx/primers4clades/index.html#0 | |
| Flexi® Vector Primer Design Tool | https://worldwide.promega.com/resources/tools/flexi-vector-primer-design-tool/ | |
| primerx | http://www.bioinformatics.org/primerx/cgi-bin/DNA_1.cgi | |
| Quant prime | http://quantprime.mpimp-golm.mpg.de | |
| RESTRİKSİYON ANALİZİ | ||
| NEBCutter | tools.neb.com/NEBcutter2/ | |
| GEN TAHMİNİ | ||
| BLASTX | http://blast.ncbi.nlm.nih.gov/ | |
| ORFFinder | www.ncbi.nlm.nih.gov/gorf/gorf.html | |
| FGENESB | http://linux1.softberry.com/berry.phtml | |
| PROTEİN | ||
| Eukaryotic Kinase and Phosphatase Database | ekpd.biocuckoo.org | |
| Human Protein Reference Database | hprd.org | |
| PROTEİN YAPISI KARŞILAŞTIRMA | ||
| ModBase | salilab.org/modbase | |
| Protein Data Bank | rcsb.org/pdb | |
| PDBe | https://www.ebi.ac.uk/pdbe/node/1 | |
| PROTEİN AİLELERİ | ||
| Pfam | pfam.xfam.org | |
| Protein Information Resource | pir.georgetown.edu | |
| POST TRANSLASYONEL MODİFİKASYONLAR | ||
| SysPTM | lifecenter.sgst.cn/SysPTM | |
| Ubiquitin and Ubiquitin-like Conjugation Database | uucd.biocuckoo.org | |
| CATH | cath.biochem.ucl.ac.uk | |
| Compendium of Protein Lysine Modifications | cplm.biocuckoo.org | |
| Database of Interacting Proteins | dip.doe-mbi.ucla.edu | |
| POST TRANSLASYONEL MODİFİKASYONLAR | ||
| PTM-SD | http://www.dsimb.inserm.fr/dsimb_tools/PTM-SD/ | |
| PRIDE | www.ebi.ac.uk/pride/archive | |
| Human Protein Atlas | https://www.proteinatlas.org/ | |
| DisProt | https://www.disprot.org/ | |
| BioGRID | https://thebiogrid.org/ | |
| NextProt | https://www.nextprot.org/ | |
| PROTEİN BİRİNCİL YAPISI | ||
| ProtParam | web.expasy.org/protparam/ | |
| PROTEİN İKİNCİL YAPISI | ||
| SOPMA | http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/ NPSA/npsa_sopma.html | |
| PSIPRED | bioinf.cs.ucl.ac.uk/psipred/ | |
| InterPro | http://www.ebi.ac.uk/interpro/ | |
| Jpred | http://www.compbio.dundee.ac.uk/jpred4/ | |
| Porter | http://distilldeep.ucd.ie/porter/ | |
| SPIDER3 | http://sparks-lab.org/server/SPIDER3/ | |
| SSPro | http://scratch.proteomics.ics.uci.edu/ | |
| HOMOLOJİ MODELLEMESİ | ||
| Swiss model | swissmodel.expasy.org/ | |
| MODELLER | https://salilab.org/modeller/ | |
| Hhpred | https://toolkit.tuebingen.mpg.de/#/tools/hhpred | |
| RaptorX | http://raptorx.uchicago.edu/ | |
| Protein Model Portal | https://www.proteinmodelportal.org/ | |
| ROBETTA | http://robetta.bakerlab.org/ | |
| FoldX | http://foldxsuite.crg.eu/ | |
| ESyPred3D | https://www.unamur.be/sciences/biologie/urbm/bioinfo/esypred/ | |
| PROTEİN ÜÇÜNCÜL YAPISI | ||
| RAMPAGE | http://mordred.bioc.cam.ac.uk/~rapper/rampage.php | |
| PROCHECK | www.ebi.ac.uk/thornton-srv/software/PROCHECK/ | |
| SAVeS | https://servicesn.mbi.ucla.edu/SAVES/ | |
| THREADING | ||
| I-TASSER | https://zhanglab.ccmb.med.umich.edu/I-TASSER/ | |
| pGenTHREADER | http://bioinf.cs.ucl.ac.uk/psipred?pgenthreader=1 | |
| GenTHREADER | http://bioinf.cs.ucl.ac.uk/psipred?genthreader=1 | |
| IntFOLD | http://www.reading.ac.uk/bioinf/IntFOLD/ | |
| Sparks X | http://sparks-lab.org/yueyang/server/SPARKS-X/ | |
| FUGUE2 | http://mizuguchilab.org/fugue/ | |
| AB INITIO YÖNTEM | ||
| FALCON | http://protein.ict.ac.cn/FALCON/ | |
| QUARK | https://zhanglab.ccmb.med.umich.edu/QUARK/ | |
| PROTEİN YAPISI GÖRSELLEŞTİRME | ||
| RASMOL | rasmol.org/ | |
| PyMOL | www.pymol.org/ | |
| RNA FRABASE | http://rnafrabase.cs.put.poznan.pl/ | |
| NPIDB | http://npidb.belozersky.msu.ru/ | |
| PROCHECK | https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/ | |
| ERRAT | http://services.mbi.ucla.edu/ERRAT/ | |
| WHAT_CHECK | http://servicesn.mbi.ucla.edu/WHATCHECK/ | |
| Verify3D | http://servicesn.mbi.ucla.edu/Verify3D/ | |
| ProSA web | https://prosa.services.came.sbg.ac.at/prosa.php | |
| WHAT_IF | http://swift.cmbi.ru.nl/whatif/ | |
| MolProbity | http://molprobity.biochem.duke.edu/ | |
| The Protein Model Portal | https://www.proteinmodelportal.org/?pid=quality_estimation | |
| SAVES | http://servicesn.mbi.ucla.edu/SAVES/ | |
| PROTEİN YAPISI HİZALAMA | ||
| SuperPose | http://wishart.biology.ualberta.ca/SuperPose/ | |
| VAST | https://www.ncbi.nlm.nih.gov/Structure/VAST | |
| TM-align | https://zhanglab.ccmb.med.umich.edu/TM-align/ | |
| MATRAS | http://strcomp.protein.osaka-u.ac.jp/matras/ | |
| PROTEİN YARIK (CLEFT) ANALİZİ | ||
| PDBsum | http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/ Generate.html | |
| MOLEKÜLER KENETLENME (DOCKING) | ||
| AutoDock4.1 | http://autodock.scripps.edu/downloads | |
| MGLTools | http://mgltools.scripps.edu/downloads | |
| ClusPro2.0 | http://cluspro.bu.edu/login.php | |
| sc-PDB | http://bioinfo-pharma.u-strasbg.fr/scPDB/ | |
| FlexX | https://www.biosolveit.de/FlexX/ | |
| GOLD | https://www.ch.cam.ac.uk/computing/software/gold-suite | |
| METABOLİK AĞLAR | ||
| Reactome | https://reactome.org/ | |
| STRING | https://string-db.org/ | |
| MINT | https://mint.bio.uniroma2.it/ | |
| BioGRID | https://thebiogrid.org | |
| Int Act | https://www.ebi.ac.uk/intact/ | |
| KEGG | https://www.genome.jp/kegg/ | |
| BioCyc | https://biocyc.org/ | |
| Ingenuity Pathways Knowledge Base (IPKB) | www.ingenuity.com | |
| Netpath | netpath.org | |
| WikiPathways | wikipathways.org | |
| İpath | pathways.embl.de | |
| BioCarta | http://amp.pharm.mssm.edu/Harmonizome/dataset/Biocarta+Pathways | |
| HumanCyc | humancyc.org | |
| The Human Protein Reference Database | hprd.org | |
| BRENDA | https://www.brenda-enzymes.org/ | |
| TRANSPATH | genexplain.com/transpath | |
| MetaCyc | https://metacyc.org | |
| METABOLOMİK | ||
| COSMOS | https://mizzou-cbmi.github.io/ | |
| ISA framework | http://isa-tools.org | |
| The Human Metabolome Database (HMDB) | www.hmdb.ca | |
| METLIN | https://metlin.scripps.edu | |
| XCMS | https://xcmsonline.scripps.edu | |
| MetaboLights Database | https://www.ebi.ac.uk/metabolights | |
| COLMAR | http://spin.ccic.ohio-state.edu/index.php/colmarm/index | |
| Fragment iDentificator | https://www.cs.helsinki.fi/group/sysfys/software/fragid | |
| MeltDB | https://meltdb.cebitec.uni-bielefeld.de | |
| MetaboAnalyst | http://www.metaboanalyst.ca | |
| MetaboMiner | http://wishart.biology.ualberta.ca/metabominer | |
| MVAPACK | http://bionmr.unl.edu/mvapack.php | |
| TRANSMEMBRAN ANALİZİ | ||
| MEMSAT | http://bioinf.cs.ucl.ac.uk/software_downloads/memsat/ | |
| MemProtMD | http://sbcb.bioch.ox.ac.uk/memprotmd/ | |
| PDBTM | http://pdbtm.enzim.hu | |
| SİNYAL PEPTİDİ TESPİTİ | ||
| SignalP | http://www.cbs.dtu.dk/services/SignalP/ | |
| Phobius | http://phobius.sbc.su.se/index.html | |
| HÜCRE ALTI YERLEŞİM | ||
| TargetP | http://www.cbs.dtu.dk/services/TargetP/ | |
| RNA ANALİZLERİ | ||
| Mfold | http://mfold.rna.albany.edu//?q=mfold/RNA-Folding-Form | |
| RNAFold | http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi | |
| Spectral Repeat Finder | http://crdd.osdd.net/raghava/srf/ | |
| YAPISAL BİYOLOJİ VERİ TABANLARI VE YAZILIMLARI | ||
| THGS: a web based database of transmembrane helices in genome sequences | http://pranag.physics.iisc.ernet.in/thgs/ | |
| PSST: protein sequence search tool | http://pranag.physics.iisc.ernet.in/psst/ | |
| CSSP: consensus secondary structure prediction | http://bioserver1.physics.iisc.ernet.in/cssp/ | |
| FAIR | http://bioserver1.physics.iisc.ernet.in/fair/ | |
| PDBj | https://pdbj.org/ | |
| Biological Magnetic Resonance Data Bank | http://www.bmrb.wisc.edu/ | |
| Pictorial analysis of macromolecular structures | www.ebi.ac.uk/pdbsum | |
| DALI | http://ekhidna2.biocenter.helsinki.fi/dali/ | |
| Vector Alignment Search Tool, | https://structure.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html | |
| CE | http://source.rcsb.org/ceHome.jsp | |
| DOMINE | manticore.niehs.nih.gov/domine | |
| SUPERFAMILY | https://supfam.org/SUPERFAMILY/ | |
| EĞİTSEL KAYNAKLAR | ||
| Train online—European Bioinformatics Institute | www.ebi.ac.uk/training/online/ | |
| MIT libraries | http://libguides.mit.edu/bioinfo | |
| Online lectures on bioinformatics | http://lectures.molgen.mpg.de/online_lectures.html | |
| Digital world biology | http://digitalworldbiology.com | |
| NIH library | https://www.nihlibrary.nih.gov/agency/nih | |
| Network science | http://www.netsci.org/Resources/Software/index.html | |
| ÖZEL VERİTABANLARI | ||
| The Arabidopsis Information Resource (TAIR) | https://www.arabidopsis.org/ | |
| FlyBase | https://flybase.org/ | |
| Glycan Fragment Database (GFDB) | http://www.glycanstructure.org/ | |
| SaccharomycesGenome Database | yeastgenome.org | |
| PomBase | pombase.org | |
| Xenbase | xenbase.org | |
| ZFIN | zfin.org | |
| TAIR | arabidopsis.org | |
| Candida Genome Database | candidagenome.org | |
| dictyBase database | dictybase.org | |
| Rat Genome Database | rgd.mcw.edu | |
| Mouse Genome Database | informatics.jax.org | |
| WormBase | wormbase.org | |
| EcoCyc | ecocyc.org | |
| miRBase | http://www.mirbase.org/ | |
| The Bacterial Diversity Metadatabase | https://bacdive.dsmz.de/ | |
| BioModels Database | https://www.ebi.ac.uk/biomodels-main/ | |
| LİGAND-BAĞLANMA BÖLGESİ-METALOPROTEİNLER | ||
| MetalPDB | http://metalweb.cerm.unifi.it/ | |
| KİMYASAL VERİ TABANLARI | ||
| Chemical Entities of Biological Interest (ChEBI) | https://www.ebi.ac.uk/chebi/ | |
| ChEMBL | https://www.ebi.ac.uk/chembl/ | |
| İLAÇ VERİ TABANLARI | ||
| DrugBank | https://www.drugbank.ca/ | |
| PharmGKB | https://www.pharmgkb.org/ | |
| ChEBI | https://www.ebi.ac.uk/chebi/ | |
| PubChem | https://pubchem.ncbi.nlm.nih.gov/ | |
| ZINC Database | https://zinc.docking.org/ | |
| Crispr VERİTABANLARI | ||
| CRISPRFinder | https://crispr.i2bc.paris-saclay.fr/Server/ | |
| CRISPRCasFinder | https://crisprcas.i2bc.paris-saclay.fr/ | |
| PILER -CR | http://www.drive5.com/pilercr/ | |
| CRISPR recognition tool | http://www.room220.com/crt/ | |
| CRISPRDetect | http://crispr.otago.ac.nz/CRISPRDetect/predict_crispr_array.html | |
| CRISPRdisco | https://github.com/crisprlab/CRISPRdisco | |
| CRISPRmap | http://rna.informatik.uni-freiburg.de/CRISPRmap/Input.jsp | |
| CRASS | https://ctskennerton.github.io/crass/ | |
| MetaCRISPR | https://github.com/hangelwen/metaCRISPR | |
| CRISPRleader | https://github.com/BackofenLab/CRISPRleader/blob/master/README.md | |
| CRISPRtionary | https://crispr.i2bc.paris-saclay.fr/CRISPRcompar/Dict/Dict.php | |
| CRISPRone | https://omics.informatics.indiana.edu/CRISPRone/ | |
| Cas-OFFinder | http://www.rgenome.net/cas-offinder/ | |
| E-CRISP | http://www.e-crisp.org/E-CRISP/ | |
| CHOPCHOP | https://chopchop.cbu.uib.no/ | |
| CRISPR-ERA | http://crispr-era.stanford.edu/ | |
| CRISPOR | http://crispor.tefor.net/ | |
| GuideScan | http://www.guidescan.com/ | |
| CASPER | http://best.snu.ac.kr/casper/ |
Referanslar:
Ibrahim, K. S., Gurusubramanian, G., Yadav, R. P., Kumar, N. S., Pandian, S. K., Borah, P., & Mohan, S. (2017). Bioinformatics – A Student’s Companion. Springer Singapore.
Shaik, N. Ahmad, Hakeem, K. Rehman, Banaganapalli, B., & Elango, R. 2019. Essentials of Bioinformatics, Volume I: Understanding Bioinformatics: Genes to Proteins. 1st ed..
Mehmet Çalıseki – Doktora Öğrencisi, Sabancı Üniversitesi.
Bilim, erdem ve azim.