The Zhao Bioinformatics Laboratory
pssRNAMiner: A Plant Short Small RNA Regulatory Cascade Analysis Server
About
Analysis
Dataset
FAQ
Location:
Analysis
Mandatory Input
Search phased small RNA clusters:
[Load demo #1 data]
Upload small RNA sequence(s) in simple format or FASTA format:
or paste sequences below:
- file / input sequence size limit: 120 MB.
- invalid small RNAs will be ignored during analysis.
Select a transcript/genomic library for mapping input small RNAs:
Arabidopsis thaliana TAIR6, cDNA, released 11/08/2005
Arabidopsis thaliana TAIR7, cDNA, released 04/25/2007
Arabidopsis thaliana DFCI Gene Index (AGI) Release 13
Arabidopsis thaliana, Genome(01/22/2004), 3.4K segments from +/- strand with 0.4K overlapped region
Brassica napus (oilseed_rape) DFCI Gene Index (BNGI) Release 3
Chlamydomonas reinhardtii DFCI Gene Index (CHRGI) Release 5
Coffea canephora (coffee) SGN unigene, ftp://ftp.sgn.cornell.edu/unigene_builds/Coffea_canephora.seq
Festuca_arundinacea (tall_fescue) DFCI Gene Index (FAGI) Release 1
Glycine max (soybean) DFCI Gene Index (GMGI) Release 12
Gossypium (cotton) DFCI Gene Index (CGI) Release 8
Gossypium (cotton) DFCI Gene Index (CGI) Release 9
Gossypium (cotton) DFCI Gene Index (CGI) Release 11
Hordeum vulgare (barley) DFCI Gene Index (HVGI) Release 9
Lycopersicon esculentum (tomato) SGN unigene, ftp://ftp.sgn.cornell.edu/unigene_builds/Tomato.seq
Lycopersicon esculentum (tomato) DFCI Gene Index (LGI) Release 11
Lotus japonicus (lotus) DFCI Gene Index (LJGI) Release 3
Medicago truncatula DFCI Gene index (MTGI) Release 8
Medicago truncatula Mt2.0 putative cDNA library, http://www.medicago.org/
Medicago truncatula Mt3.0 putative cDNA library plus MTGI9
Nicotiana benthamiana DFCI Gene Index (NBGI) Release 2
Nicotiana tabacum (tobacco) DFCI Gene Index (NTGI) Release 3
Nicotiana tabacum (tobacco) SGN unigene, ftp://ftp.sgn.cornell.edu/unigene_builds/Nicotiana_tabacum.seq
Oryza sativa (rice) TIGR genome cDNA OSA1 Release 5(OSA1R5)
Oryza sativa (rice) DFCI Gene index (OGI) Release 17
Oryza sativa (rice) OSA1R5 Genome, 3.4K segments from +/- strand with 0.4K overlapped region
Oryza sativa (rice) MSU Rice Genome Annotation, version 7
Physcomitrella patens (moss) JGI Gene Transcripts V1.1, http://genome.jgi-psf.org/Phypa1_1/Phypa1_1.download.ftp.html
Populus trichocarpa (poplar) JGI Gene Transcripts V1.1, http://genome.jgi-psf.org/Poptr1_1/
Populus trichocarpa (poplar) JGI Gene Transcripts 210 / part of Phytozome v9.0, ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Ptrichocarpa/annotation/
Populus trichocarpa (poplar) DFCI Gene Index (PPLGI) Release 3
Populus trichocarpa (poplar) Genome Assembly R1.0, 3.4K segments from +/- strand with 0.4K overlapped region
Solanum tuberosum (potato) DFCI Gene Index (STGI) Release 11
Triticum aestivum (wheat) DFCI Gene Index (TAGI) Release 9
Vitis vinifera (grape) DFCI Gene Index (VVGI) Release 5
Zea mays (maize) DFCI Gene Index (ZMGI) Release 17
Mapping ambiguity (
maximum hits on transcript/genomic library
):
Maximum offset from phased position (+/- nt):
Your Email (optional):
Optional Input
Identify phase-initiator for detected small RNA clusters:
[Load demo #2 data]
Candidate phase-initiators in FASTA format (miRNA/ta-siRNA):
- accept up to 0.2 MB valid sequences.
Maximum expectation for searching complimentary fragment:
Max distance from cleavage site to phased small RNA clusters (nt):
Start position of cleavage site in complimentary fragment (nt):
End position of cleavage site in complimentary fragment (nt):
© 2008 by The Samuel Roberts Noble Foundation, Inc.