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Submit amino acid sequence for analysis by PDLoc

Description

       This is a server for plasmodesmata localizing protein prediction using a combined Support Vector Machine and Hidden Markov Model.

The model is described in

• Jiefu Li, Jung-Youn Lee, and Li Liao. (2019). Detecting de novo Plasmodesmata targeting signals and identifying PD targeting proteins. ICCABS'19 (9th IEEE International Conference on Computational Advances in Bio and medical Sciences), Miami, FL, USA.
  

Input

    The program takes proteins in FASTA format. Example is given below.

>5H2A_CRIGR | you can have comments after the ID
MEILCEDNTSLSSIPNSLMQVDGDSGLYRNDFNSRDANSSDASNWTIDGENRTNLSFEGYLPPTCLSILHLQEKNWSALLTAVVI
ILTIAGNILVIMAVSLEKKLQNATNYFLMSLAIADMLLGFLVMPVSMLTILYGYRWPLPSKLCAVWIYLDVLFSTASIMHLCAIS
LDRYVAIQNPIHHSRFNSRTKAFLKIIAVWTISVGVSMPIPVFGLQDDSKVFKQGSCLLADDNFVLIGSFVAFFIPLTIMVITYFLTIK
SLQKEATLCVSDLSTRAKLASFSFLPQSSLSSEKLFQRSIHREPGSYTGRRTMQSISNEQKACKVLGIVFFLFVVMWCPFFITNIMA
VICKESCNEHVIGALLNVFVWIGYLSSAVNPLVYTLFNKTYRSAFSRYIQCQYKENRKPLQLILVNTIPALAYKSSQLQAGQNKDS
KEDAEPTDNDCSMVTLGKQQSEETCTDNINTVNEKVSCV

Output

    This tool gives a table of the input protein IDs alongside their prediction scores and their sequences. The sequences are highlighted to show important regions. The regions in red, light blue, and green represent different sections of the JMe region. The region in red represents the alpha region, where the first targeting signal is located. The region in light blue represents the beta region, where the second targeting signal is located. The region in green represents the gamma region, where no predicted targeting signal exists. The region in blue represents what we predict as the transmembrane domain that is closest to the C-terminal end of the protein. The options for binary or exploratory mode will affect which proteins are shown in the final results. In binary mode, only proteins above a certain score threshold will be shown. In exploratory mode, (unsure about this part) all proteins will be shown along with their probability of localizing to the plasmodesmata.

Here is an example:

ID	Score	Sequence
PDLP2_ARATH	-67.016	MGLSISFLSIIMMMCLLFPDLNVVVKSATTEYTTLIYKGCARQQFSDPSGLYSQALSAMFGSLVSQSTKTRFYKTTTGTSTTTITGLFQCRGDLSNHDCYNCVSRLPVLSDKLCGKTIASRVQLSGCYLLYEVSGFSQISGMEMLFKTCGKNNIAGTGFEERRDTAFGVMQNGVVSGHGFYATTYESVYVLGQCEGDVGDTDCSGCVKNALEKAQVECGSSISGQIYLHKCFIAYSYYPNGVPRRSSSSSSSSSSSSSGSSNSDPSTSTGATGKTAIIVGGAAGVGFLVICLLFAKNLMRKKHDDY
PDLP3_ARATH	-69.96769	MGFYSLKQLLLLYIIIMALFSDLKLAKSSSPEYTNLIYKGCARQRLSDPSGLYSQALSAMYGLLVTQSTKTRFYKTTTGTTSQTSVTGLFQCRGDLSNNDCYNCVSRLPVLSGKLCGKTIAARVQLSGCYLLYEISGFAQISGMELLFKTCGKNNVAGTGFEQRRDTAFGVMQNGVVQGHGFYATTYESVYVLGQCEGDIGDSDCSGCIKNALQRAQVECGSSISGQIYLHKCFVGYSFYPNGVPKRSSPYPSSGSSGSSSSSSSSGTTGKTAIIVGGTAGVGFLVICLLFVKNLMKKKYDDY