MotifLab
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Application data |
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| Created by | Kjetil Klepper |
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| Biological application domain(s) | Sequence analysis, Gene regulation, Transcription factors and regulatory sites, Transcription factors and regulatory sites, Sequence motifs, ChIP-seq |
| Principal bioinformatics method(s) | Sequence motif discovery, Sequence contamination filtering, Genome visualisation, Visualisation, Format conversion, Peak calling |
| Created at | Norwegian University of Science and Technology (NTNU) |
| Maintained? | Yes |
| Input format(s) | 2bit, BED, BigBed, BedGraph, BigWig, Bioprospector, CSV, Delimited Text, Excel, FASTA, GFF, GTF, JASPAR, MEME, Plain text, WIG, XMS, TRANSFAC, Custom Motif format, Custom, Others |
| Output format(s) | BED, BedGraph, Bioprospector, CSV, Delimited Text, Excel, FASTA, GFF, GTF, HTML, JASPAR, MEME, Plain text, WIG, XMS, TRANSFAC, Custom Motif format, Custom, Others |
| Software features | Complete motif discovery workbench: import DNA sequences and download additional data tracks from UCSC Genome Browser, visualize tracks in the integrated genome browser, perform de novo motif discovery or search for instances of known motifs, use operations to pre- and post-process data tracks, explore the data interactively with various analysis tools, automatically record all your steps in protocols that can be executed as workflows |
| Programming language(s) | Java |
| Licence | Freeware |
| Operating system(s) | platform-independent |
| Contact: | kjetil.klepper@ntnu.no |
Summary: MotifLab is a general workbench for analysing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules within a rich graphical interface.
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Description
MotifLab is a general workbench for analyzing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. MotifLab can improve performance of binding site predictions by allowing users to integrate several motif discovery tools as well as different types of data, for instance phylogenetic conservation, epigenetic marks, DNase HS sites, ChIP-seq data, positional binding preferences of transcription factors, TF-TF interactions, TF-expression and target gene expression.
With more than 40 data-processing operations available, users can create, import, export, transform and manipulate data objects such as DNA sequences, numeric- or region-based data tracks, transcription factor binding motifs, regulatory modules, background models, text- and numeric-variables, and collections and partitions of data objects.
Various statistical analyses can be applied to evaluate or compare data objects and results can be output in many common text-based data formats or in HTML with images included. Interactive tools allow users to search for and highlight interesting features of datasets, for instance potential networks of binding sites for interacting transcription factors.
The program is written in JAVA and can either be run in interactive mode with a graphical user interface providing powerful data visualization capabilities, or the analysis to be performed can be defined in a protocol-script and executed by MotifLab in batch-mode from a command-line interface. The latter option allows MotifLab to be incorporated as a component in larger data processing pipelines.
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References
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