DFAM : Multiple alignment and profile HMMs of repetitive DNA RELEASE 1.1 -------------------------------------- 1. INTRODUCTION Dfam is a collection of conserved DNA element sequence alignments, hidden Markov models (HMMs) and matches lists for complete genomes. This first release focuses on models for Human, but the list of genomes and models will expand rapidly. 2. LOCATIONS Dfam is available on the web at: http://dfam.janelia.org/ 3. STATISTICS Dfam 1.1 consists of 1143 models that match 50% (bal bp) of the Human genome. 4. CONSTRUCTION OF DFAM Dfam is based on a fixed sequence database called Dfamseq - Dfamseq 1.0 is currently just the Human genome, (GRC37.p7, downloaded from http://www.ensembl.org) containing 3102 Mb of DNA. Sequence alignments for human interspersed repeat families were built using annotation on the UCSC genome browser (http://http://genome.ucsc.edu/, Human build hg19), which itself depends on annotation software RepeatMasker (http://http://www.repeatmasker.org/) and the database of repeat consensus sequences, RepBase (http://www.girinst.org/repbase/). For each family, annotated instances were transitively aligned based on mutual alignment to the Repbase consensus sequence. Hidden Markov models (HMMs) were constructed from the sequence alignment using the HMMER3 tool hmmbuild, and each model was then searched against Dfamseq using a beta version of the HMMER3 tool nhmmer, with hit metadata (sequence location, score, etc) captured for distribution. Note: We are currently using a pre-release of HMMER 3.1. The source code for this snapsort is available for the Dfam FTP site. 5. DESCRIPTION OF CHANGES FROM RELEASE 1.0 (internal) to 1.1 1. Updated the version of nhmmer that reduces over-extension. 2. Redundancy between the hits has now been flagged in the databse. 3. Searches are now down to an E-value of 100. We the least stringent E-value that can be used for the gathering threshold has been relaxed to an E-value of 10. 6. FUTURE FORMAT CHANGES No major changes for the format of the flatfile planned for next release. 7. DESCRIPTION OF RELEASE FILES relnotes.txt - This file. userman.txt - A fuller description of Dfam fields. Dfam.hmm - Dfam HMMs in an HMM library, searchable with the nhmmer program. Dfam.seed - Annotation and seed alignments of all Dfam entires in Stockholm format. Dfam.hits - TSV list of all matches from dfamseq that score above the GA threshold. diff - A list of files for each entry that have changed since the last release. dfamseq - The underlying sequence database in fasta format. hmmer.src - The source code of the current beta version of nhmmer used to make this release. 8. DESCRIPTION OF FIELDS See userman.txt for more detailed description of each field Compulsory fields: ------------------ AC Accession number: Accession number in form DFxxxxxxx. ID Identification: One word name for entry. DE Definition: Short description of entry. AU Author: Authors of the entry. SE Source of seed: The source suggesting the seed members belong to one entry. GA Gathering method: Score used for sequences within the clade specified by MS. TC Trusted Cutoff: Score used for sequences outside the clade specified by MS. NC Noise Cutoff: Smaller cutoff than GA; not used in Dfam. FR False Discovery Rate: Target FDR used to set GA. BM Build method SM Internal search method MS Model specificity: TaxID and TaxName, based on NCBI taxonomy. CT Classification tags: Repeat Type, Class, and Superfamily. SQ Sequence: Number of sequences in alignment. // End of alignment. Optional fields: ---------------- DC Database Comment: Comment about database reference. DR Database Reference: Reference to external database. RC Reference Comment: Comment about literature reference. RN Reference Number: Reference Number. RM Reference Medline: Eight digit medline UI number. RT Reference Title: Reference Title. RA Reference Author: Reference Author RL Reference Location: Journal location. PI Previous identifier: Record of all previous ID lines. CC Comment: Comments. WK Wikipedia Reference: Reference to wikipedia. SN Synonym A widely accepted alternative name for the model. CN Classification Note: A free text comment about the model classification. 9. REFERENCES Papers on Dfam are listed below: Dfam: a Database of Repetitive DNA Based on Profile Hidden Markov Models Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AFA, Finn RD NAR, submitted 10. THE DFAM CONSORTIUM Dfam is maintained by a consortium of researchers. You can contact the Dfam consortium at: dfam "at" janelia.hhmi.org The current members of the Dfam consortium are: Robert D. Finn, Jody Clements, Sean R. Eddy, Thomas A. Jones, Travis J. Wheeler: Janelia Farm Research Campus, USA Arian F. A. Smit, Robert Hubley: Institute for Systems Biology, USA Jerzy Jurka: Genetic Information Research Institute, USA 11. ACKNOWLEDGEMENTS R.D.F., J.C, S.R.E, T.A.J., and T.J.W received institutional support from HHMI Janelia Farm Research Campus. J.J. was supported by grants from the National Library of Medicine, National Institutes of Health (P41LM006252-12). A.F.A.S and R.H were supported by a grant from the National Institutes of Health (RO1 HG002939). 12. COPYRIGHT NOTICE Dfam - A database of conserved DNA element alignments and HMMs Copyright (C) 2012 The Dfam consortium. This database is free; you can redistribute it and/or modify it as you wish, under the terms of the CC0 1.0 license, a 'no copyright' license: The Dfam consortium has dedicated the work to the public domain, waiving all rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. See Other Information below. Other Information o In no way are the patent or trademark rights of any person affected by CC0, nor are the rights that other persons may have in the work or in how the work is used, such as publicity or privacy rights. o Unless expressly stated otherwise, the Dfam consortium makes no warranties about the work, and disclaims liability for all uses of the work, to the fullest extent permitted by applicable law. o When using or citing the work, you should not imply endorsement by the Dfam consortium. You may also obtain a copy of the CC0 license here: http://creativecommons.org/publicdomain/zero/1.0/legalcode ___________________ The Dfam Consortium 2012