Since the last time, we have used ABySS to assemble the single read data of P. andina, with several different k-mers, and looked at the N50 and E-size values to somewhat determine the quality of the contigs.
Below is two graphs where the k-mer sizes have been plotted against N50 and E-size, respectively.
Different k-mer sizes plotted against the corresponding N50 values. The highest N50 value corresponds to a k-mer of 23.
Different k-mer sizes plotted against the corresponding E-size values. The highest E-size value corresponds to a k-mer of 23.
Based on what we see here, using a k-mer of 23 seems like the best option for now. We did not see any difference in these parameters for the trimmed data using the tool sickle. After meeting with Lars Arvestad today, this is one of the things we brought up, and as we understood it, the data has already been trimmed from e.g. adapters, and therefore trimming it again does not make any real difference.
After the meeting, and after explaining what we had done so far and the results we had obtained, we could conclude that the assembly is more or less done and that the scaffolding part indeed is not possible as expected (since we do not have paired reads). The purpose of our assembly is therefore not to 100% assemble the whole genome, but rather to create contigs large enough for a whole genes to fit inside it, and hopefully those will be the CHS-genes. The problem with not being able to access the CHS-gene files was also solved during the meeting as Lars gave us access.
During a group meeting after the meeting with Lars, we sat down and started preparing the presentation for Seminar 2.
In this presentation we have focused on the three main tasks that define the project, and also what we have done so far and some issues that we have had. The presentation is not finished at the time of writing as we will work during the weekend and probably add more results.
To conclude what we have done so far in the project:
- Assembled the P. andina reads into contigs
- Evaluated which size of k-mer that gives highest N50 and E-size values
- Further defined the project and what tasks we have left
- Obtained and looked at the CHS-gene files. I though it was going to be DNA-sequences, but it was protein sequences which means we will just have to use the tBLASTn tool.
- Further divided the work and almost finished the Assembly description (one of the deliverables of the project).
Upcoming days
The main goal is now to finish Task 2 which is the identification of CHS genes. The CHS-gene file contains genes from four different species (all possible hybrids with P. andina):
- P. infestans
- P. sojae
- P. ramorum
- Saprolegnia parasitica
CHS-gene.fa (Click to view)
>chs_Psoj1 Phytophthora sojae
MSGAPPPSSGFAPRSYGQQPLSHAPRSSMMSVEYDGIPLPPPSIRSCGSQQYVTSYIPTGAAFPPSSVQDMISSMKSYASATDLVRTYSEIPSVEEALSTLDRAAAALNARRYRDALKLYLEGGYAMANVAERQANPKICNLLTSKGFETLNWCARLCDWIEGRIKEKHPRPGVHKVGIPVSNWDEDWVGPFMDEEEARRMWYTPVYCPHPIDFSNLGYRLRCVETGRRPRLMICITMYNEGPQQLKATLKKLANNLAYLKEQMPGDEKSLTGAFAGDDVWQNVLVCIVADGREQVHPKTLDYLEAIGLYDEDLLTINSAGIGAQCHLFEHTLQLSVNGKCLLPIQTVFALKENKASKLDSHHWYFNAFAEQIQPEYTAVMDVGTMLTKSALYHLLFAFERNHQIGGACGQLTVDNPFENLSNWVISAQHFEYKISNILDKSLESCFGFISVLPGAFSAYRYEAIRGAPLDAYFQTLNIELDVLGPFIGNMYLAEDRILSFEVVARKNCNWTMHYVKDAVARTDVPHDLVGLISQRKRWLNGAFFATLFSIWNWGRIYSESKHTFVRKMAFLVFYVYHLLYTAFGFFLPANLYLALFFIVFQGFQQNRLEFIDTSEYSQTVLDCAVYIYNFSYLFGLLMLIIIGLGNNPKHMKLTYYFVGAVFGLMMMLSSLVGAGIFFSTPATVHSIVVSILTVGVYFIASALHGEVHHIFMTFTHYTALIPSFVNIFTIYSFCNLQDLSWGTKGLHDDPLLAASLDETEKGDFKDVIAKRRALEELRREEKERVENRKKNFEAFRTNVLLTWAFSNLIFALFVVYFASSSTYMPVLYIFVASLNTCRLLGSIGHWVYIHTEGLRGRVIDKSECGNGTGRYPQNSYVQLEEHYAALAEDQRTYASGRTNASVRTVNDVSSAA
>chs_Psoj2 Phytophthora sojae
MEQDGGGYVSSNAEEYDAAPSSGLPTPDGPDVWRDTRPTSHSYVDEPHANQPIERQLSYRQPGLNPAAEETYEAAFRLIQLAADAERSGSPLQAIQLYTDAGDVLIKVGKREPDPLLKQGIRQKANEIMKRAEELDEWYYSVQESARKAALPPQLQIQRTQVPRVQEAWQGRKPTLSQAPEFTHMRYTAVSTKDPVKFSDDGFQLRVEEAGKKIRVFITITMYNEEGSELQGTLKGIARNLEFMAEQWGDRAWESVAVAVVSDGRTKASASCLDFLAGLGAFDEEIMTVTSMGVDVQLHLFEATVQLVRDDNFESFYPPIQLIYALKENNAGKLNSHLWFFNAFSEQLLPTYTVLVDVGTIPGPTSIFKLIRSMDRNPQIGGVAGEIAVDHPNYFNPVIAAQHFEYKISNIMDKSLESVLGFISVLPGAFSAYRYEAIRAEKGVGPLPEYFKSLTTSTRDLGPFKGNMYLAEDRILCFELLARRGRNWTMHYVKDAIARTDVPETLVDLIKQRRRWLNGSFFAGLFAISNFSRVWKESGHSLSRKIVLTLQFIYLSVQNVLSWFLLSNLFLTFYYVLTLTLYSKYPALLAIVLGIYLAIVGGIVVFALGNRPEKRTAAFYSFSYVFMGLVMLVVSVISIYGLVADVSVTDPRDDLASCSVSNFELVGGVVTAIGLVFASAFIHGEFSVLLSTLQYYFMLPTFVNILGIYAYSNLHDLSWGTKGLETAGHGAAKVAQGNGNLKEIVAQQKRIEAEKQRAAQEKEDVDNSFRAFRSSLLLFWLVTNAVWMYCMTYFVSSSCYLKFISYVVAVFNVVRFFGSAVFLCFRIARRLGTCGASRSGKSGRNYQAHLPAEWQAHYKRSSNATTETTTTGNGQQTYVGLNISDLSSPAATNYRNMEEVR
>chs_Pram1 Phytophthora ramorum
MSGGPPPSSGFVPRSFGLPPISQAPRSSMMSVEYDGIPLPPPSIRSCGSQQYVTSYIPTGAAFPSGSVQEMISSMKSYASATDLVRTYSEIPSVEEALVTLDRAAVALNARRYRDALKLYLEGGYAMANVAERQANPKICNLLTSKGFETLNWCARLCDWIEGRIKEKHPRPGVHKVGIPVSNWDEDWVGPYLDEEEARRMWYTPVYCPHPIDFSNMGYRLRCVETGRRPRLMICITMYNEGPQQLKATLKKLANNLTYLKEQDSGHDKALSETFKGNDVWQNVLICIVADGREQVNDKMLDYLEAVGLYDEDLLTINSAGIGAQCHLFEHTLQLSVNGKCLLPIQTVFALKETKSNKLDSHHWYFNAFAEQIQPEFTAVMDVGTMLTKSALYHLLFAFERNHQIGGACGQLTVDKPFENLSNWVISAQHFEYKISNILDKSLESCFGFISVLPGAFSAYRYEAIRGAPLDAYFQTLNVDLDVLGPFIGNMYLAEDRILSFEVVARKNCNWTMHYVKDAVARTDVPHDLVGLISQRKRWLNGAFFATLFSIWNWGRIYSESSHTFTRKVAFLVFYGYHLLYTAFGFFLPANLYLALFFIVFQGFQQNRLQFIDTSDFSQTVLDCAVYIYNFAYLFGLLMLIIIGLGNNPKHMKLTYYFVGAVFGVMMMLSSLVGLGIFFSTPATINSIVVSILTVGVYFIGSALHGEMHHIFMTFTHYTALIPSFVNIFTIYSFCNLQDLSWGTKGLHDDPLLAASLDETEKGDFKDVIAKRRAMEERRREEKERTDNRKKNFEAFRTNVLLTWAFSNLILALFVVYFTDSSTYMPILYYFVASLNSCRLLGCIGHWVYIHTDGLRGRVLDKTECGNGTGRYPQNSYIQLDEHYAALVEDQRTYASGRTNASVRTNNDISSAA
>chs_Pram2 Phytophthora ramorum
MSNGRSTEDLRARLQSLRASRTSSLQPQEAARDWGDTFQPGELEELQSMLEQDAAGDFSSGTEEYDAIASSGLSTPDNVDVWRDTRPTSHSYVDEPHPNQPIERQLSYRQSGLNPAVEETYEAAFRLIQLAAEAERSGTPLQAIQLYTDAGDVLVKVGRREPDPLLKQGIREKANEIMKRAEELDEWYYSVQESARKAALPPQLQIQRTQVPRVQEAWQGRKPTLNQPPEFTHMRYTAVSTKDPVKFTDDGFQLRIEQAGKKIRVFITITMYNEEGSELQGTLTGIARNLEFMAEQWGDRAWESVAVAVVSDGRTKASASCLDFLTGLGAFDEEIMTVTSVGVDVQLHLFEATVQLVRDDNFESFYPPIQLIFALKESNAGKLNSHLWFFNAFSEQLLPTYTVLVDVGTIPGPTSIFKLIRSMDRNPQIGGVAGEIAVDHPNYFNPVIAAQHFEYKISNVMDKSLESVLGFISVLPGAFSAYRYEAIRAEKGVGPLPEYFKSLTTSTRDLGPFKGNMYLAEDRILCFELLARRGRSWTMHYVKDAIARTDVPETLVDLIKQRRRWLNGSFFAGLFAISNFSRVWRESGHSLSRKLVLTLQFVYLGVQNLLSWFLLSNLFLTFYYVLTLTLYSDYPVLLAIVLGIYLVIVGGIVVFALGNRPEKRTAAFYSFSYVFMGLVMLVVSVISIYALVADISVTDPRDDLASCSVSNFELVGGVATAIGLVFASAFIHGEFSVLLSTLQYYFMLPTFVNILGIYAYSNLHDLSWGTKGLETAGHAAAKVTQGNGNLKEIVAQQKRLEALKQRAAEEKEDVDNSFRAFRSSLLIFWLVTNAVWMYCMTYFVSSSCYLKLISYVVAVFNMARFLGSAVFLCFRIARRLGACGTVRSGASGRNYQASLPIEWQAHFKHSSNTTTETTTRNGHIGLNMSDLSSPVATNYKNMEEAM
>chs_Pinf Phytophthora infestans
MSGAPPPSSGFQPRSIGLPPLSHGPRSSMMSVEYDGIPLPPPSIRSCGSQQYVTSYIPTGAAFPSGSVQDLISSMKSYASATDLVRTYSEIPSVEEALVTLDRAAVALGARRYRDALKLYLEGGYAMANVAERQANPKICNLLTSKGFETLNWCARLCDWIEGRVKEKHPRPGVHKVGIPVSNWDEDWVGPYLDEEEARRMWYTPVYCPHPIDFSNMGYRLRCVETGRRPRLMICITMYNEGPQQLKATLKKLANNLAYLKEQKKDHEKTLSRDFAGDDVWQNVLLCIVADGREQVNDKMLDYMEAIGLYDEDLLTINSAGIGAQCHMFEHTLQLNVNGKSLLPIQTVFALKESKSSKLDSHHWYFNAFAEQIQPEYTAVMDVGTMLTKSALYHLLFAFERNHQIGGACGQLTVEKPFENLSNWVISAQHFEYKISNILDKSLESCFGFISVLPGAFSAYRYEAIRGAPLDAYFQTLNIDLDVLGPFIGNMYLAEDRILSFEVVARKDCKWTMHYVKDAVARTDVPHDLVGLISQRKRWLNGAFFATLFSIWNWGRIYSESNHSFTRKMAFLVFYLYHLLYTAFTFFLPANLYLALFFIVFQGFQQNRLEFVDTSEYSQTVLDCAVYMYNFVYLFGLLMLIIIGLGNNPKHMKLTYYFVGAVFGVMMMLSSLVGMGIFFSTPATTHSIVVSILTVGVYFIGSALHGELHHIFMTFTHYTALIPSFVNIFTIYSFCNLQDLSWGTKGLHDDPLLAASLDETEKGDFKDVIAKRRAMEERRREENERMENRKKNFEAFRSNVLLTWTFSNLIFALFVAYFADSSTYMPILYIFVASINSCRLLGCIGHWIYIHTTGLRESFLDKSECGNGTGRYPQNSYVQLDEHYAALAEDQRTYASGRTNASVRTNNDVSSIA
>chs_Spar1 Saprolegnia parasitica
MPPKRPTEASGRRYAPPAGRPSNNAANAKPRAPRKGVSSRASNVPSAASSYEYDYEYNMMPMMQAPPKSQPTFLSNIAPISAKEASMKGSNAMQLLLQGTSFTIDDAFRAIERAIQAENEGRFREALKHFLDGGEMIVTAAEKEASQKVRNLLLHKGKEVLEWAEHLAEWIERYNTSTPPVRIAKPMAVEVTYDRTMNSPDLDETEARMMFYTPVCSGPKAFTETGYRLQCIQSGRRPRLMVVITMYNEDENELRSTLRKVCNNVLYLKQHSLPGYEGDDAWKQVLVVVVSDGRTKANKGTLEWLANVGLYDEDVMNITSTGVKVQCHLFEHSLQMTKENSIRFPPLQLDSHLWYFDAFAEQIMPDYTVLLDVGTMPTKSSFYKLLTALEINAQIGGVCGEIAVDKPLPNMCNWVIAAQHFEYKISNILDKSLESCFGFISVLPGAFSAYRYKAIRGAPLQAYFKSLTTDMAELGPFAGNMYLAEDRILCFELLARKDCNWTMHYVKDAIARTDVPTNLIDLVGQRRRWLNGSFFATLFAIWNWGRVYTESNHSLTRKLALLVHALLGVSAANFYLALYFVIFQGFRDNRWNFIDTSEYPQWVLDGLPTAFNVFYAVTVFTQVTIGLGNKPKHVKGTHYLISVLFGLLMLLASGVAIVIFITSSKDAMAIVLAVLILGTFFIGSALHCEVHHIVLTFVQYTALMPSFVNILMVYSFCNLHDLSWGTKGIDTGHEAHKTEAVGQYKDIVARQKALEAKKAQDARNQDELKKRFDSFRSNLLLVWVMSNMSMVIICVNTVGADSFLPFLYAFVAAFNGIRLLGCIGYLIYYARQFLLFNTLSATGVLHKRHEARKHKKAEDPDPIDMELGTFNEPATSEIGAPMMQAPYNRMR
>chs_Spar2 Saprolegnia parasitica
MSDSNLDLAARLRALREGGAEPAPAPAPTPYMHSPPSRTRPTPLYTQESLEFGGTYTTGSPVGAEADGVYTQVPVWKDSKEKTYGYLDDEPAPQAQTLLNKANDLVQRQASNKAFRRQHTAAFRPLPNTVEELLDGSPTYEGAFRLVQLAVQMEQDGDPQAAINLYADAGATLVEVGRKEVDPLLQKGIRQKAQELLQRAEDLEAWMNGVAEEARKAALPPSLRIARTNVPTVEQTWAGRPPPFHDANEFKLMRYTAVATKDPIQFSDDGYVLRVHELQRPIKVFITITMYNEEGSEIKGTLTGLAKGLAYMCKEYGDDFWQQVAVAIVSDGRTKASKTCLEYLKAVGAFDEEIMTVTSLGVDVQMHLFESTLQLVENQNFEAYYPPLQVIYALKENNGGKLNSHLWFFNAFSEQLNPKYTVLVDVGTIPAETSVFRLIRSMERNAQIGGVAGEIAVEAPNFFNPVIAAQHFEYKISNIMDKSLESVFGFISVLPGAFSAYRYEAIRAVKGVGPLPEYFKSLTSTTKELGPFQGNMYLAEDRILCFELLARKQRRWTMHYVKDAIARTDVPETLVDLIKQRRRWLNGSFFAGLFAIGHFGRVWSQSSHSFGRKLVFTFQFVYLALQNLLSWFLLSNLFLTFYFVLTLAFTESAPALLQTMLTVYLAIIGGLIVFALGNKPEPRTASFYLFSCLYMGIIMLLVTGISIYGLIGKGTSAVKDPRTITGIFSNCTVSDAELAGGVITSLGLIFLSAFVHGEFGILLSFVQYFFMLPTFVNVLGIYAYSNLHDLSWGTKGLESGGGHGPAKAGGGNVKDVVEQQKKIEAARQAAAREKEDVDNSFRAFRSTLLLSWLTTNGIWLYVVTDYMSSGCYLKGLSYIVGFFNVVRFTGCVVFVILRMFRRFGCGARASRDNYQEALPAEWQTHYNVTNRTDGRVAPPPKHAASMDPTTPHGGVYQQV
>chs_Spar3 Saprolegnia parasitica
MGVPTLSKASVFRFARQPRHHGVKTRLLRSRSKTLMLGGQSTAETAQYASCNPNGDETSSNSLKPLKLKDMSTDDLLRHAEQLDMHLAKIYIESQKTKALAPIVTKSIGLPQQLWEDAGVAPPYHSAAEFQDLRYTAVRTADPIAFSADGYSLRVHTLGKSIKVFITVTMYNEPASQLQATLTGLAGGIDYLCHQYGYDFWQEVAVVVVADGRSKTHHSVLPYLESFGAFEKNLLAQAIAASKDTHVHLFESTIQLRKTNGSFHAPMQLIFALKEHNAGKLHSHLWFFNAFSEQVDPTYTALVDVGTVPAESSVYRLIRSMERNPQIGGVAGEIAVDDPDFFNPVIAAQHFEYKIANIMDASLQSVFGFIGVLPGAFSAYRYEAIRPINGVGPLAEYFKSLTASKKELGLCVGNMYLAEDRILCFEILARKNCDWTMHYVKDAIAHTDVPETLVDLIKQRRRWLNGSFFAGLFAIWNFGRVWTQSAHSLPRKCAFSLQFLYLAFQNVMNWFLLSNLFLTFFYILSLALYYKSIELLHVVLGTYFVLVGSLIVFALGNKPGHRTAIYYRVSSYIMGTIMLCVTCISLYALLGNVQFVDPRSDLPSCSVSNYELEAGAFFSLGIIFVCAFMHGEFGIVRSTVQYFFMLPTFVNVLGIYAYSNLHDLSWGTKGIETSAGHNGLPTSKFGSVKDMVALHLNATSTTDVVSEADKRKGVVAAEHEDVDNRFRVFRSLLLLTWLLTNGCWLYYATSFISCSCYLKYLSYIVAVFNTFRFLGGLLFLSFRMARGALHCCRQGVKKTRPLRCGNPQAGDDCSPV
>chs_Spar4 Saprolegnia parasitica
MTTLPERLLARVTSSMSALGGTAKLVTAQEGFRLIEQGVLAERQQHYKEAVDRFLGAAGVLDAVAATEADLHVRRLLHAKASDVVAWTEGIVAWMQHRPEVRPAYPPRQSKGISMPTTTVSAATLAFGMDEVERTSLHYTPVLTRSPSEFSRDGYELQVLRRHRRPRMLIVITMYNEDGSEIEATLRKVGNNVAYLCRHDLPGYEGELAWQNVLVVIVSDGRAKASASTLITLREMGVYDEDTLRITSAGLATSMHLFERTLLLPEAPGAKKLWTHTSETMPPLQVVFALKEENAGKLHSHLWFFHGFCNQVDPTYTVLLDVGTLPTKSALYKLVSAMEVNQQVGGVCGEIAVSQPLPHLTSLIISTQHYEYKISNVLDKATESCFGFISVLPGAFSAYRFKAIQGAPLDAYFKSLTTDMLALGPFQGNMYLAEDRILCFELLARKNCSWTMMYVKDAIARTDVPTTLVDLMAQRRRWLNGSFFAMLYTIFNWGRVYSEARHSLCRGLALLVQYTFMTVQVVFNWFLVANFYLTVYYVIFYALERNALGVLDTRAFYASHGALAKGLFNVVYGLVFVVQIILGMGNRPKHVARTYRAIGAYYMLLVVLTTAASVLTLVHTGAAALAPKEIALGIAVFGVYFIAAACHCELHHIVLSFVQYSLLLPVMINTLTIYSFCNLQDLSWGTKGIDTSSHDTGASENGEYKDVVARQKAAEDRAKQAAATTDLVRRRFDSFRSNLLLLWLVSNAALVGGLLYGALLDVYLPCLFVAIGAFNTYRLLGSLLFLLYTGRQWLLLQLCLCCGCLRRRYDRERRRGSDDRTMAILSPRDPLATI
>chs_Spar5 Saprolegnia parasitica
MVSSQLSTGLPAIARRPSVRSTRVGSHVRNDNDCVTTVDAFRYIERGVRAEYDMFYSEAINCFVNAGECLLIVAEQNDDDVSQMLLAKSQEVIGWAEELSIWLENGRAGPLPSRNCRGIQIPFTKEYEGGEHYEEAAELSYTPVATVNPINFTLDGYRMQCVTRGRKPTMMLVITMYNEDGAELAQTLRKVCNNVKYIQKNALPGYEGDDAWQNIVVCIVSDGRTKANPSATSFLRDIGVFNEDAMTIFSSGAATQMHLFERTVRLAKDPLNKQSVIMSNNSTIGADYPPLQMVYALKEHNAGKLNSHLWFFNAFCNQVDPEYNILLDVGTLPTKAALYKLLATLEMKADIGGVCGEIAVSRPIPNLWNFVIATQHFEYKVSNLLDKATESCFGFVSVLPGAFSAYRFAAIKGAPLQAYFKSLTTDMAELGPFYGNMYLAEDRILCFELLARTNGAWKLKYIKDAVARTDVPSTLVDLMAQRRRWLNGSFFAMLYSIVQWGRLYSHTNHSLFTKAGLLIQYFQLLVQLFFGWFMCGFFYLSVYYVVFTTLKKSKLPFWDSEEWYDDHHSMAMSIFNIVYAFLIMVQIIFGLGNKPKHVKWLYTFLSIFYAIVVITAVFFSVCSLSSHNGMSSFNIVLLAATFGVYFIAAAFHFELHHVVFTFVQYLVMLPTTINILMIYAFCNIQDLSWGTKGLGDSAGHGPTKGGGQRLGSGGYSDLVAQRKAAEAAARHDAVVADQVRRRFDSFRSYTLLFWLISNALLIMTCIYFVGANVFLPSLFLFIALFNVTRLLGSIAFVLATGRDWLLLKLCLCSGGMAKRKQKKEKVKDQDGFGALDSSKVLRHSA
>chs_Spar6 Saprolegnia parasitica
MSRRNYAPAARGGNGPRPNMNPANMGPPPQMPPPQHGSGRNLRAPPPRQVQQQGSFDRDSDDDMYGQHGANGVLGVPVWQDSAAYEHGSYLQENTPPSQRIPYPGPQGGGMMPPPGGMMPPPQQFAPAPVRMLNAGALQNQSNQQMQVMRDSNVGQAVPASTPEAFRIIASGVTAEAEARYQSAVNDFLAGGEMLALVSEREADPHIRSLLNTKAIQVLEWSKNLHDWYQQGMRGPMPRRFVGKIGVNVVNRLGACAGRIDAGSPSELRTMYYTPAANKVVSDFTKDGYRLQCIEEGRTPQLMVVITMYNEDQVEMYSTLKKVANNIAHIKSQKLPGYEGDDAWKNILVVIVSDGRTKANKGTLAFLRDVGAFDEDVMNILMVGVDVMCHVFEFCVQLKKANTIEASASSSERYPPTQVVFALKEHNGGKLNSHEWYFNAFAEQIQPEYTVLLDVGTMPTAKAFYLLLCAMEIDPQIGGTCGEIAVDKPIPHLCNWVIAAQHFEYKISNVMDKSLESVFGFISVLPGAFSAYRYKAIRGAPLEAYFKSLTTPMNELGPFQGNMYLAEDRILCFELLARRNCRWTMQYVKDAIARTDVPTDLVALIGQRRRWLNGSFFALVYTILNWGRVYTESNHSYIRKFFLCIQYAYMTANVALSWVLPANFFLVTYFLVIVGFKQNNWGYIPTSGIPENTKDIIVQVFSLLYGTSFLIQLVAGLGNKPKHIKGVYRLTAVFYALVMLLTSVIAFGFIMKPWIDSLRSGVPFAAMVTSFEIKDIAAFVASVGVFFLASCLHCEMHHIAMSFIQYMCLLPTFVNILNTYSFCNLHDLSWGTKGLESSDGHGPKAGGGGNYKDAAEAKKAEEARKKKEGEIKDKMEGDFQYFRSKLLIFWLLSQMGFAYLIISFDSVNGQEGANYLKFLFYIVAGFNLFRLFGSTYFLLIEARICVEKMCIRGTMRDRLKAKKKKQAIRAAQTQHVFor the next meeting, which will take place on Monday the 11th after Seminar 2, we plan to have done the following:
- Panos will run the assembly again with a k-mer of 23 as this is the contigs we will use in further tasks
- We will all BLAST CHS-genes against the assembled contigs of P. andina to assess whether CHS-genes can be found among the contigs or not. Panos will BLAST the P. infestans genes, I will BLAST P. sojae and P. ramorum genes, and Maria will BLAST the S. parasitica genes. This will done using the tool tBLASTn and aligning two sequences (this is the plan so far).
- If genes are found or not within the contigs, we will have evaluated what that means and try and draw conclusions about the relatedness of P. andina and other species within the Oomycetes family.
- Finish the Seminar 2 presentation.
Additionally, after presenting to each other what we have found individually, we plan to start with the next task which is to take out the largest contig and BLAST that against the P. infestans genome which was assembled in 2009. We will also look into the tool MUMmer which should already be available at UppMax for the comparison of contigs.