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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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Maintainers


  • person_outline Peter Svensson <>
  • person_outline Karl Ekwall <>

Publication for POsitioning DataBase and Analysis Tool

Podbat in publications

 (8)
PMCID: 5017727
PMID: 27611590
DOI: 10.1371/journal.pgen.1006238

[…] 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 […]

PMCID: 5341516
PMID: 26902262
DOI: 10.15252/embr.201541866

[…] 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 […]

PMCID: 4687421
PMID: 26518661
DOI: 10.15252/embr.201541214

[…] 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. […]

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

[…] 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 […]

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 […]


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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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