Ders 9: NCBI - GEO Uygulamaları - Biyoinformatik-Lab

Querying GEO DataSets and GEO Profiles

http://www.ncbi.nlm.nih.gov/geo/info/qqtutorial.html#conq

Exercises

http://cys.bios.niu.edu/yyin/teach/PBB2013/Jan29-2013.pdf

GEO introductory tutorial v3 - bioconnector.virginia.edu
http://www.ncbi.nlm.nih.gov/geo/info/geo_paccess.html#ExampleI

Ders 8: Ensembl - BioMart Uygulamaları - Biyoinformatik-Lab

BioMart Homepage http://www.ensembl.org/biomart/martview/0d24ff71b7966a5a36c01188bcbb5bc0

Linkteki çalışmayı tamamlayınız.
https://docs.google.com/forms/d/1PHrlOB997QDtXLgspSOue6qR2x8RmtRICIRhTdtcOco/viewform

Ek Çalışma:

Ders 7: NCBI - UniGene Uygulamaları - Biyoinformatik-Lab

UniGene Homepage: http://www.ncbi.nlm.nih.gov/unigene

Linkteki çalışmayı tamamlayınız. https://docs.google.com/forms/d/1_DgEWuv3gHZeBLCgAFcHHhQBAkRuicwNVLEkTZRSHLU/viewform

Ders 6: Multiple Sequence Alignment Uygulamaları - Biyoinformatik-Lab

Multiple Sequence Alignment Homepage: http://www.ebi.ac.uk/Tools/msa

Linkteki çalışmayı tamamlayınız.
https://docs.google.com/forms/d/1lXRibDoizmV05k0M9UVNOMzoUFKdIbxQ0IYyiZXz_1M/viewform?usp=send_form

Protein Dizileri

>gi|6288724|gb|AAF06717.1|AF078906_1 interleukin 7 receptor alpha chain [Mus musculus]
MMALGRAFAIVFCLIQAVSGESGNAQDGDLEDADADDHSFWCHSQLEVDGSQHLLTCAFN
DSDINTANLEFQICGALLRVKCLTLNKLQDIYFIKTSEFLLIGSSNICVKLGQKNLTCKN
MAINTIVKAEAPSDLKVVYRKEANDFLVTFNAPHLKKKYLKKVKHDVAYRPARGESNWTH
VSLFHTRTTIPQRKLRPKAMYEIKVRSIPHNDYFKGFWSEWSPSSTFETPEPKNQGGWDP
VLPSVTILSLFSVFLLVILAHVLWKKRIKPVVWPSLPDHKKTLEQLCKKPKTSLNVSFNP
ESFLDCQIHEVKGVEARDEVESFLPNDLPAQPEELETQGHRAAVHSANRSPETSVSPPET
VRRESPLRCLARNLSTCNAPPLLSSRSPDYRDGDRNRPPVYQDLLPNSGNTNVPVPVPQP
LPFQSGILIPVSQRQPISTSSVLNQEEAYVTMSSFYQNK
>gi|4504679|ref|NP_002176.1| interleukin 7 receptor [Homo sapiens]
MTILGTTFGMVFSLLQVVSGESGYAQNGDLEDAELDDYSFSCYSQLEVNGSQHSLTCAFE
DPDVNTTNLEFEICGALVEVKCLNFRKLQEIYFIETKKFLLIGKSNICVKVGEKSLTCKK
IDLTTIVKPEAPFDLSVIYREGANDFVVTFNTSHLQKKYVKVLMHDVAYRQEKDENKWTH
VNLSSTKLTLLQRKLQPAAMYEIKVRSIPDHYFKGFWSEWSPSYYFRTPEINNSSGEMDP
ILLTISILSFFSVALLVILACVLWKKRIKPIVWPSLPDHKKTLEHLCKKPRKNLNVSFNP
ESFLDCQIHRVDDIQARDEVEGFLQDTFPQQLEESEKQRLGGDVQSPNCPSEDVVVTPES
FGRDSSLTCLAGNVSACDAPILSSSRSLDCRESGKNGPHVYQDLLLSLGTTNSTLPPPFS
LQSGILTLNPVAQGQPILTSLGSNQEEAYVTMSSFYQNQ
>gi|11230786|ref|NP_068687.1| interleukin 21 receptor [Mus musculus]
MPRGPVAALLLLILHGAWSCLDLTCYTDYLWTITCVLETRSPNPSILSLTWQDEYEELQD
QETFCSLHRSGHNTTHIWYTCHMRLSQFLSDEVFIVNVTDQSGNNSQECGSFVLAESIKP
APPLNVTVAFSGRYDISWDSAYDEPSNYVLRGKLQYELQYRNLRDPYAVRPVTKLISVDS
RNVSLLPEEFHKDSSYQLQVRAAPQPGTSFRGTWSEWSDPVIFQTQAGEPEAGWDPHMLL
LLAVLIIVLVFMGLKIHLPWRLWKKIWAPVPTPESFFQPLYREHSGNFKKWVNTPFTASS
IELVPQSSTTTSALHLSLYPAKEKKFPGLPGLEEQLECDGMSEPGHWCIIPLAAGQAVSA
YSEERDRPYGLVSIDTVTVGDAEGLCVWPCSCEDDGYPAMNLDAGRESGPNSEDLLLVTD
PAFLSCGCVSGSGLRLGGSPGSLLDRLRLSFAKEGDWTADPTWRTGSPGGGSESEAGSPP
GLDMDTFDSGFAGSDCGSPVETDEGPPRSYLRQWVVRTPPPVDSGAQSS
>gi|7212777|gb|AAB20029.2| erythropoietin receptor; EPOR [Mus sp.]
MDKLRVPLWPRVGPLCLLLAGAAWAPSPSLPDPKFESKAALLASRGSEELLCFTQRLEDL
VCFWEEAASSGMDFNYSFSYQLEGESRKSCSLHQAPTVRGSVRFWCSLPTADTSSFVPLE
LQVTEASGSPRYHRIIHINEVVLLDAPAGLLARRAEEGSHVVLRWLPPPGAPMTTHIRYE
VDVSAGNRAGGTQRVEVLEGRTECVLSNLRGGTRYTFAVRARMAEPSFSGFWSAWSEPAS
LLTASDLDPLILTLSLILVLISLLLTVLALLSHRRTLQQKIWPGIPSPESDFEGLFTTHK
GNFQLWLLQRDGCLWWSPGSSFPEDPPAHLEVLSEPRWAVTQAGDPGADDEGPLLEPVGS
EHAQDTYLVLDKWLLPRTPCSENLSGPGGSVDPVTMDEASETSSCPSDLASKPRPEGTSP
SSFEYTILDPSSQLLCPRALPPELPPTPPHLKYLYLVVSDSGISTDYSSGGSQGVHGDSS
DGPYSHPYENSLVPDSEPLHPGYVACS
>gi|5853248|gb|AAD54385.1|AF178684_1 class I cytokine receptor [Homo sapiens]
MPAGRRGPAAQSARRPPPLLPLLLLLCVLGAPRAGSGAHTAVISPQDPTLLIGSSLLATC
SVHGDPPGATAEGLYWTLNGRRLPPELSRVLNASTLALALANLNGSRQRSGDNLVCHARD
GSILAGSCLYVGLPPEKPVNISCWSKNMKDLTCRWTPGAHGETFLHTNYSLKYKLRWYGQ
DNTCEEYHTVGPHSCHIPKDLALFTPYEIWVEATNRLGSARSDVLTLDILDVVTTDPPPE
VHVSRVGGLEDQLSVRWVSPPALKDFLFQAKYQIRYRVEDSVDWKVVDDVSNQTSCRLAG
LKPGTVYFVQVRCNPFGIYGSKKAGIWSEWSHPTAASTPRSERPGPGGGACEPRGGEPSS
GPVRRELKQFLGWLKKHAYCSNLSFRLYDQWRAWMQKSHKTRNQDEGILPSGRRGTARGP

DNA Dizileri
http://www.foodmicrobe.com/Fig1.txt

Ekstra Çalışma
http://www.molgen.ua.ac.be/bioinfo/course/exercises_alignment-example.html

Ders 5.1 : Uygulama Örnekleri - Biyoinformatik-Lab

http://www.molecularevolution.org/resources/activities/fasta_blast_activity
http://www.smbi-maroc.org/smbieng/EMBL-EBI/PracticalEBI/UniProt_Tutorial_V1.1_Tangier.pdf