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BIOINF 10-035: Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions

Cornelius Schmidtke, Sven Findeiß, Cynthia M. Sharma, Juliane Kuhfuß, Steve Hoffmann, Jörg Vogel, Peter F. Stadler, Ulla Bonas

If you have problems accessing electronic information please contact sven [at] bioinf [dot] uni-leipzig [dot] de

Rfam Prediciton

Predictions using Rfam database version 10.0 and rfam_scan.pl Script (e-value 100)
annotation filefasta file
BED FASTA

RNAcode Predicition

annotation filefasta file
high scorring segments: BED (20,187 entries p<0.05) FASTA (20,187 entries p<0.05)
short ORFs: BED (24 entries; RNAcodeID_? indicate alternativ ORFs) FASTA (24 entries; RNAcodeID_? indicate alternativ ORFs)

Raw Sequencing Data

454 pyrosequencing was performed on a Roche 454 sequencer using FLX and Titanium chemestry. For each a terminator exonuclease treated (Xcv+, library 2 in the publication) and an untreated (Xcv-; library 1 in the publication) library has been prepared and sequenced. Xcv+ is enriched for primary transcripts (most sRNAs and mRNAs) whereas the Xcv- library contains both primary and processed RNA sequences.


Descriptionfasta filegzip compressed fasta file
Terminator exonuclease treated library sequenced on a 454 sequencer using FLX chemestry. The 5' linker is already clipped. Note that the poly(A) and/or 3' linker is still attached. Xcv+_454_GS_FLX.mfa Xcv+_454_GS_FLX.mfa.gz
Library sequenced on a 454 sequencer using FLX chemestry. The 5' linker is already clipped. Note that the poly(A)-tail and/or 3' linker is still attached. Xcv-_454_GS_FLX.mfa Xcv-_454_GS_FLX.mfa.gz
Terminator exonuclease treated library sequenced on a 454 sequencer using Tianium chemestry. The 5' linker is already clipped. Note that the poly(A)-tail and/or 3' linker is still attached. Xcv+_454_Titanium.mfa Xcv+_454_Titanium.mfa.gz
Library sequenced on a 454 sequencer using Tianium chemestry. The 5' linker is already clipped. Note that the poly(A)-tail and/or 3' linker is still attached Xcv-_454_Titanium.mfa Xcv-_454_Titanium.mfa.gz

Annotated Transcription Start Sites

comlplete data set

annotation fileinformation file
chromosome (NC_007508): BED (1372 entries, p<0.05) CSV (1372 entries, p<0.05)
plasmid (NC_007507): BED (49 entries, p<0.05) CSV (49 entries, p<0.05)

5 prime UTRs (>10 nt)

annotation filefasta file
chromosome (NC_007508): BED (695 entries) FASTA (695 entries)
plasmid (NC_007507): BED (18 entries) FASTA (18 entries)

Leaderless Transcripts (UTR <=10 nt)

annotation filefasta file
chromosome (NC_007508): BED (118 entries) FASTA (118 entries)

sRNAs identified in this study

antisense RNAs

clustalw filefasta fileadditional information
asX1 ALN FASTA -
asX2 ALN FASTA only found in XCV and Xanthomonas axonopodis pv. citri
asX3 ALN FASTA -
asX4 ALN FASTA -
asX5 - FASTA XCV specific
asX6 ALN FASTA found on the large plasmid in XCV and a plasmid of Xanthomonas axonopodis pv. citri
asX7 ALN FASTA 10 copies found Stenotrophomonas maltophilia K279a but only 1 in S. maltophilia R551-3

intergenic sRNAs

clustalw filefasta fileadditional information
sX1 ALN FASTA five copies in XCV; paralogous to sX10
sX2 ALN FASTA -
sX3 - FASTA XCV specific
sX4 ALN FASTA -
sX5 ALN FASTA -
sX6 ALN FASTA high scoring segement predicted by RNAcode EPS
sX7 ALN FASTA -
sX8 ALN FASTA phylogeny suggests a ~80nt transcript found in various species rather than the 118 nt transcript found in XCV
sX9 ALN FASTA only present in XCV and Xanthomonas axonopodis pv. citri 306
sX10 ALN FASTA five copies in XCV; paralogous to sX1
sX11 ALN FASTA -
sX12 ALN FASTA -
sX13 ALN FASTA -
sX14 ALN FASTA -
sX15 ALN FASTA 10 copies found Stenotrophomonas maltophilia K279a but only 1 in S. maltophilia R551-3
6S RNA ALN FASTA houskeeping RNA; conserved in much more species