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Podbat specifications

Information


Unique identifier OMICS_04868
Name Podbat
Alternative name POsitioning DataBase and Analysis Tool
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU Lesser General Public License version 2.1
Computer skills Advanced
Version 0.6.4
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline Peter Svensson
  • person_outline Karl Ekwall

Publication for POsitioning DataBase and Analysis Tool

Podbat citations

 (7)
call_split

Pfh1 Is an Accessory Replicative Helicase that Interacts with the Replisome to Facilitate Fork Progression and Preserve Genome Integrity

2016
PLoS Genet
PMCID: 5017727
PMID: 27611590
DOI: 10.1371/journal.pgen.1006238
call_split See protocol

[…] s, 3’ and 5’ UTRs, promoters, tRNAs, centromeres, 5S rRNAs, long terminal repeats, and the mating type loci from PomBase []. We also considered the locations of meiotic DSB hotspots [], NDRs [] using podbat [], origins of replication [], the 500 most highly expressed genes from expression data collected across several growth conditions [], and G4 motifs []. For Pfh1 and Cdc20 sites, regions within […]

library_books

Regulating retrotransposon activity through the use of alternative transcription start sites

2016
EMBO Rep
PMCID: 5341516
PMID: 26902262
DOI: 10.15252/embr.201541866

[…] (http://www.bioconductor.org) packages “affy”, “affxparser”, and “preprocessCore” with standard parameters. CEL‐files were imported and quantile normalized as described in .Data was visualized using Podbat , R, and the Integrated Genome Browser (IGB, Affymetrix). R was used to generate average gene occupancy graphs. Box‐and‐whisker plots were created in R using the “boxplot” function with standar […]

library_books

The Paf1 complex factors Leo1 and Paf1 promote local histone turnover to modulate chromatin states in fission yeast

2015
EMBO Rep
PMCID: 4687421
PMID: 26518661
DOI: 10.15252/embr.201541214

[…] ufacturer's instructions. Raw data from the Hiseq (fastq files) were aligned to ASM294v2 using Bowtie2 using default parameters. The ASM294v2.24 annotation was downloaded from pombase.org and used in Podbat. The aligned data (sam files) were imported and normalized to million reads. Data from independent biological duplicates were averaged. Identical reads were discarded to remove PCR artifacts. S […]

library_books

Panspecies Small Molecule Disruptors of Heterochromatin Mediated Transcriptional Gene Silencing

2015
PMCID: 4301722
PMID: 25487573
DOI: 10.1128/MCB.01102-14

[…] eneChip Whole Target labeling and hybridization protocol (Affymetrix). The data were normalized with quantile normalization plus scaling using Tiling Analysis Software (TAS) 1.1 and imported into the Podbat browser program (). Podbat was used to produce upregulated gene lists for the different treatments using settings for various fold changes and a P value of <0.05. GeneSpring GX software (Agilen […]

library_books

The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G quadruplex motifs to prevent DNA damage

2014
BMC Biol
PMCID: 4275981
PMID: 25471935
DOI: 10.1186/s12915-014-0101-5

[…] , essential genes, highly expressed genes [], origins of replication from OriDB [], telomeres (Webb and VAZ, submitted), LTRs, 5S rRNA, tRNAs, centromeres, NDRs [see Additional file ] [] called using Podbat [], rDNA repeats and meiotic DSB hot spots []. Unless otherwise noted, these annotations were taken from PomBase []. The highly transcribed genes were determined from the RNA-seq data collected […]

library_books

DNA Topoisomerase III Localizes to Centromeres and Affects Centromeric CENP A Levels in Fission Yeast

2013
PLoS Genet
PMCID: 3597498
PMID: 23516381
DOI: 10.1371/journal.pgen.1003371

[…] sing a bandwidth of 100 and assigned to S. pombe genome coordinates (Sanger 2007 and Sanger 2004 for centromeres). Browser images were generated using Integrated Genome Browser (IGB) (Affymetrix) and PodBat (www.podbat.org). Podbat was used for averaging signals across ORFs and IGRs, for comparing gene lists and for moving averages (bandwidth 100 probes, step size 20 probes) after alignment of gen […]

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Podbat institution(s)
Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
Podbat funding source(s)
Supported by grants from the Swedish Cancer Society, the Goran Gustafsson foundation for research in natural sciences and medicine and the Swedish research council.

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