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General Back to top

WebScipio offers an advanced option to map cDNA data (EST or mRNA) on the exon-intron gene structure reconstructed by Scipio. Based on this mapping alternative splice forms are predicted.

Options Back to top

Data

Different cDNA data files can be choosen for different species. An autocompletion field offers the possibility to search for a species. Then an EST or mRNA data file needs to be selected.

Sequence type

In the first step of the cDNA alignment the cDNA data is either aligned to the coding DNA of the gene, the translation of the coding DNA or the whole genomic DNA (including introns). In the second step it is always aligned to the genomic DNA.

BLAT Tile Size

Sets the size of match that triggers an alignment. Usually between 8 and 12. Default is 11 for DNA and 5 for protein.

BLAT Step Size

Spacing between tiles. Default is Tile Size.

BLAT Min. Identity

Sets minimum sequence identity (in percent) between cDNA sequence and gene sequence.

BLAT Min. Score

Sets minimum score. This is the matches minus the mismatches minus some sort of gap penalty. If the the min. score is set to a high value, only long cDNA hits are taken into account.

BLAT Min. Match

Sets the number of tile matches. Usually set from 2 to 4. Default is 2 for nucleotide, 1 for protein.

BLAT Max. Gap

Sets the size of maximum gap between tiles in a clump. Usually set from 0 to 3. Default is 2. Only relevent for minMatch > 1.

BLAT One Off

If set to 1 this allows one mismatch in tile and still triggers an alignments.

Examples Back to top

Drosophila melanogaster Myosin 7B gene with alternatively spliced exons

OrganismDrosophila melanogaster
Genome file chromosome v 5.0.0
YAML-file for uploadDownload_button ScipioResult_Dm_DSCAM.yaml
Query sequenceMSEFVRQHGEYVWVKPQNTTSEFAVPFGARIVRTEKTQTLVCDDRNKQFWVPAGDVLKAM
HITSQEDVEDMITLGDLQEYTILRNLQNRYAKQLIYTYTGSMLVAINPYQILPIYTNREI
QLYRNKSLAELPPHIFAISDNAFQRLQRLKENQCVVISGESGAGKTESTKLILQYLAAIS
GKHSWIEQQIIEANPIMEAFGNAKTVRNDNSSRFGKYIEIRFTPQGAIQGARIQQYLLEK
SRIVFQSRDERNYHIFYCMLAGLSTAERERLKLQEQSPSQYHYLAQGGCFTLPGRGDAKD
FADIRAAMKVLSFKPEEVWSILSLLAAILHLGNLRFTATEVANLATAEIDDTPNLQRVAQ
LLGIPISALNAALTQRTIFVHGEHVTTSLSKEAAIEGRDAFVKSLYDGIFVRIVRRINET
INKQVDQPMNSIGVLDIFGFENFDNNSFEQLCINYANENLQQFFVGHIFKMEQDEYQNEH
INWQHIEFQDNQQILDLIGMKPMNLMSLIDEESKFPKGTDQTLLEKLHVQHGNRSIYVKG
KTTQTSLFGIRHYAGVVMYNPLGFLEKNRDSFSGDLRTLVQRSTNKYLVDIFPHEMPMDT
AKKQPTLCVKFRNSLDMLMRTLSQAHPYFIRCIKPNEYKEPKNFDKELCVRQLRYSGMME
TARIRRAGYPIRHAYRAFVERYRLLVPPVGPLEQCDCRKLARQICEVALPADSDRQYGKT
KLFLRDEDDASLELQRSQLMLKSIVTIQRGIRRVLFRRYMKRYREAIITVQRYWRGRLQR
RKYQVMRQGFHRLGACIAAQQLTTKFTMVRCRTIKLQALSRGYLVRKDFQKKLLERRKQN
QLKKEELLKLAKMKEAEELLRLQQLKEQKEREQREQQEKRLQEEQRLKAEAAARNALAMA
AVQQKRRTKPVKQEAPKAPTLQARNSLPPPPTTLIVAAPLPTRPASAVTRINTIPESPGT
IDVESSKQMVDDVFRFLNDEPDAALRKLNNISSGDTIRLPKSVPNNIDTSDFSYLKYAAT
YFGGGATAQHERKPLKKSLLKHEHPIDEMASKAIWLTILRFMGDLPDVVSSPTLHVFDNE
NLMSDLASLLNTSDSYKPRLFVRQSQRRIPKPLASGEKEAQEFYQHWLNVPTSHLEKIHF
IIGHGIIKNSLRDEILAQICKQLYLNPSRSSYSRGWLLLSLCLSCFPPSKEFEPHLRSFM
KQGTAQLQATPSLQRLERTLVNGPRCQPPSLFELHAIRGRHPLRLDIHLMDGQQRRLQVD
AASTAREAVNQLCQGMGLTDTFGFGLVMSLNGKLMPLGAGQEHVLDAISECEQRQLDAPW
KLYIRKEMFATWYDPSMDPKATQLIYKQILNGLKCGEYRCRSEKDIAMVCALACFVEYGP
GEILRLKPSEITAFVPSDLLAPGERAIENWSRLIAATYEKSSYVKEEQNDLLLEAQKRAK
EDICLFAHLSWPMRHSRLFEVVRKEGPKLQSDELMLGINSAGLFLIDETEQVLASCCFSE
VLKVHVESDDKLHVMTFQHVNFVLQCSSAQDANEVINYMLDNLRQRSSYGVALDPVVEGD
LEDCLVLNPGDLIEFEAGVTGAQLMAGNAQDCYRGCVNGQWGQFLAGNVRVLATLTKPSE
KLQDILREGRFQEPPKPTPRANYSRRRQHNISQLAESHFREPLDSDKAPLSKFSPEPLKA
PLLKAVVKVPPLFQQALVMHHHILKYMGDIARSNLPVNTDLIFQPALQHPLLCDELYCQL
MKQLSDNPSSESEKRGWDLLYLATGLVAPSVLVMRELIILLRMRADALADACLKRLKRSL
AQGQRKKAPHLIEVEGIQQRCLHIYHKIYFPDDTVEAFEIESHTRGAELIADIAQRLELK
SPVGYSIFLKTGDRVYAMPEEEFVFDFITQLIYWLRQQRTIRSISDGQYQLHFMRKLWLN
NHPGEDLNGDMIFSYPQELHKYLKGYYPIDCEQASRLAILVYSADHDVSLQRLPEVLTRL
IPEDLIPLQTVAEWRQQILPKVHRDHLTEDHAKILFLQELSHFACFGSTFFVVKQQNDDA
LPETLLIAINSTGFHMLDPTTKEILRSYEYSQLGIWSSGKNHFHIRFGNMIGASKLLCST
TQGYKMDDLLASYVKYFNEHE
Expert optionsGap to Close = 15 aa
Search for Alternatively Spliced Exonsdefaults
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Result

Activity diagrams Back to top

Detailed diagram of the cDNA search algorithm

Activity diagram of the search for alternatively spliced exons
link to kassiopeia
link to diark
link to cymobase
link to motorprotein.de
MPG
MPI for biophysical chemistry
Uni-Goettingen
Informatik Uni-Goettingen