bioinformatics.bris.ac.uk
Software - Computational Genomics Group
http://www.bioinformatics.bris.ac.uk/software.html
The Mogrify resource predicts how to trans-differentiation from any human cell type to any other human cell typeby perturbing the transcriptional network. Mogrify includes all cell types from the FANTOM5. Database contains assignments of protein domains of known structures to all completely sequenced genomes. The library of hidden Markov models and the software required to run the SUPERFAMILY assignment procedure is available from the downloads page. There is a very low traffic mailing list. A community ...
supfam.cs.bris.ac.uk
SUPERFAMILY database of structural and functional protein annotations for all completely sequenced organisms
http://supfam.cs.bris.ac.uk/SUPERFAMILY/index.html
SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes. The SUPERFAMILY annotation is based on a collection of hidden Markov models. Which represent structural protein domains at the SCOP. Superfamily level. A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from over 2,478 completely sequenced genomes. Against the hidden Markov models. Submit sequences for SCOP classification.
supfam.org
SUPERFAMILY database of structural and functional protein annotations for all completely sequenced organisms
http://www.supfam.org/SUPERFAMILY/index.html
SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes. The SUPERFAMILY annotation is based on a collection of hidden Markov models. Which represent structural protein domains at the SCOP. Superfamily level. A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from over 2,478 completely sequenced genomes. Against the hidden Markov models. Submit sequences for SCOP classification.
fantom.gsc.riken.jp
FANTOM - Software
http://fantom.gsc.riken.jp/software
Links and description of various software used in FANTOM. A directory of defined factors for direct cell reprogramming. AVAILABILITY: http:/ www.mogrify.net/. DOI: 10.1038/ng.3487. A pipeline for detecting waves of coordinated transcriptional regulation in gene expression time-course data. AVAILABILITY: The CIDER source code and the validation datasets are available on request from the corresponding author. Delve version 0.95. A probabilistic short read aligner used in FANTOM5 and ENCODE. CAGExploreR is ...
bioinformatics.bristol.ac.uk
Software - Computational Genomics Group
http://www.bioinformatics.bristol.ac.uk/software.html
The Mogrify resource predicts how to trans-differentiation from any human cell type to any other human cell typeby perturbing the transcriptional network. Mogrify includes all cell types from the FANTOM5. Database contains assignments of protein domains of known structures to all completely sequenced genomes. The library of hidden Markov models and the software required to run the SUPERFAMILY assignment procedure is available from the downloads page. There is a very low traffic mailing list. A community ...
