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Dfam

Dfam 2.0 (September 2015, 4150 entries). The Dfam database is a collection of Repetitive DNA element. Sequence alignments, hidden Markov models (HMMs). For complete Eukaryote genomes. More. You can find data in Dfam in various ways. Analyze your DNA sequence for Dfam matches. Paste your DNA sequence here to find matching Dfam entries. This search will search against all Dfam models ( regardless of clade ) and using the trusted cut-off thresholds (stringent). You can set your own search parameters here.

http://www.dfam.org/

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Dfam | dfam.org Reviews
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Dfam 2.0 (September 2015, 4150 entries). The Dfam database is a collection of Repetitive DNA element. Sequence alignments, hidden Markov models (HMMs). For complete Eukaryote genomes. More. You can find data in Dfam in various ways. Analyze your DNA sequence for Dfam matches. Paste your DNA sequence here to find matching Dfam entries. This search will search against all Dfam models ( regardless of clade ) and using the trusted cut-off thresholds (stringent). You can set your own search parameters here.
<META>
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1 browse
2 download
3 and matches lists
4 quick links
5 sequence search
6 example
7 view a sequence
8 homo sapiens
9 mus musculus
10 danio rerio
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browse,download,and matches lists,quick links,sequence search,example,view a sequence,homo sapiens,mus musculus,danio rerio,drosophila melanogaster,caenorhabditis elegans,keyword search,jump to,dfam consensus,citing dfam,nucleic acids research,posts
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Dfam | dfam.org Reviews

https://dfam.org

Dfam 2.0 (September 2015, 4150 entries). The Dfam database is a collection of Repetitive DNA element. Sequence alignments, hidden Markov models (HMMs). For complete Eukaryote genomes. More. You can find data in Dfam in various ways. Analyze your DNA sequence for Dfam matches. Paste your DNA sequence here to find matching Dfam entries. This search will search against all Dfam models ( regardless of clade ) and using the trusted cut-off thresholds (stringent). You can set your own search parameters here.

INTERNAL PAGES

dfam.org dfam.org
1

Dfam

http://www.dfam.org/help

Each entry or model in Dfam is represented on the website is represented by a single page. If you wish to stably link to this entry page, please use the Dfam accession, such that the URL looks like: http:/ dfam.org/entry/DFXXXXXXX. Each entry page is divided into five tabs, found below the family identifier and accession. A one line description of the entry. Of the RPH filter). Pertinent database cross references. This plot shows how matches to an articial benchmark sequence not containing any TE inserti...

2

Dfam

http://www.dfam.org/about

Dfam is a database of repetitive DNA elements organized around profile hidden Markov models (HMMs) built using alignments generated by the most-used TE annotation tool, RepeatMasker. Using the database of the TE database, Repbase. Dfam version 2.0 was produced at the Univerity of Montana. And the Institute for Systems Biology. Dfam is built upon on a sequence database called dfamseq, which contains reference assemblies ( including non-placed contigs and mitochondrial DNA ) for human [ hg38. And fly [ dm6.

3

Index of /web_download/

http://www.dfam.org/web_download

Index of /web download/. 28-Oct-2015 20:27 - Publications/. 02-Oct-2015 01:15 - Release/. 28-Oct-2015 00:00 - Tools/.

4

Dfam

http://www.dfam.org/browse

You can use the links below to find lists of entries which begin with the chosen letter (or number) or view all the entries on one page. Send a mail to help@dfam.org.

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cryptogenomicon.org cryptogenomicon.org

Cryptogenomicon | Genome sequence analysis, the HMMER and Infernal projects, and the Eddy/Rivas lab | Page 2

https://cryptogenomicon.org/page/2

Genome sequence analysis, the HMMER and Infernal projects, and the Eddy/Rivas lab. Newer posts →. HMMER mission control: we are go for launch vehicle separation(s). June 2, 2015. Were officially launched today. At the EMBL European Bioinformatics Institute (EBI). In Cambridge UK. You can read an EBI press release here. This marks the completion of the pilot HMMER server project at Janelia Farm and its transition to the EBI. All of this has been led by Rob Finn,. Because of the terrifyingly sophisticated ...

cryptogenomicon.org cryptogenomicon.org

Janelia Farm | Cryptogenomicon

https://cryptogenomicon.org/category/janelia-farm

Genome sequence analysis, the HMMER and Infernal projects, and the Eddy/Rivas lab. Category Archives: Janelia Farm. September 11, 2014. Belated congratulations to Rob Finn, who has moved to EMBL-EBI to lead the Protein Families team. The HMMER web services pilot project. That HHMI has funded at Janelia, under Rob’s leadership, is now in transition to EBI, and Rob and I will write more about this in the future. This fall. The nhmmer software project and his lead role in the Dfam mobile element database.

cryptogenomicon.org cryptogenomicon.org

Congratulations | Cryptogenomicon

https://cryptogenomicon.org/category/congratulations

Genome sequence analysis, the HMMER and Infernal projects, and the Eddy/Rivas lab. September 11, 2014. Belated congratulations to Rob Finn, who has moved to EMBL-EBI to lead the Protein Families team. The HMMER web services pilot project. That HHMI has funded at Janelia, under Rob’s leadership, is now in transition to EBI, and Rob and I will write more about this in the future. This fall. The nhmmer software project and his lead role in the Dfam mobile element database. It’s getting a little underp...

cryptogenomicon.org cryptogenomicon.org

Exodi | Cryptogenomicon

https://cryptogenomicon.org/2014/09/11/exodi

Genome sequence analysis, the HMMER and Infernal projects, and the Eddy/Rivas lab. September 11, 2014. Belated congratulations to Rob Finn, who has moved to EMBL-EBI to lead the Protein Families team. The HMMER web services pilot project. That HHMI has funded at Janelia, under Rob’s leadership, is now in transition to EBI, and Rob and I will write more about this in the future. This fall. The nhmmer software project and his lead role in the Dfam mobile element database. It’s getting a little underp...

repeatmasker.systemsbiology.net repeatmasker.systemsbiology.net

Download and Mailing List Subscription Page

http://repeatmasker.systemsbiology.net/RMDownload.html

Unix system with perl 5.8.0 or higher installed. RepeatMasker uses a sequence search engine to perform it's search for repeats. Currently Cross Match, RMBlast and WUBlast/ABBlast are supported. You will need to obtain one or the other of these and install them on your system. For Cross Match go to http:/ www.phrap.org. You will want to select "Phred/Phrap/Consed" as Cross Match is part of the Phrap package. For HMMER please download the v3.1b2. Version here: http:/ hmmer.org/. Unpack the distribution in ...

repeatmasker.org repeatmasker.org

Download and Mailing List Subscription Page

http://www.repeatmasker.org/RMDownload.html

Unix system with perl 5.8.0 or higher installed. RepeatMasker uses a sequence search engine to perform it's search for repeats. Currently Cross Match, RMBlast and WUBlast/ABBlast are supported. You will need to obtain one or the other of these and install them on your system. For Cross Match go to http:/ www.phrap.org. You will want to select "Phred/Phrap/Consed" as Cross Match is part of the Phrap package. For HMMER please download the v3.1b2. Version here: http:/ hmmer.org/. RepeatMasker will now work ...

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Dfam

Dfamjanelia.org is moving on August 31. The dfam website will be moving to it's new location at http:/ dfam.org. Please update your bookmarks and scripts now. Dfam 1.4 (May 2015, 1306 entries). The Dfam database is a collection of Repetitive DNA element. Sequence alignments, hidden Markov models (HMMs). For complete Eukaryote genomes. More. You can find data in Dfam in various ways. Analyze your DNA sequence for Dfam matches. Paste your DNA sequence here to find matching Dfam entries. View a Dfam Entry.

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dfam.org dfam.org

Dfam

Dfam 2.0 (September 2015, 4150 entries). The Dfam database is a collection of Repetitive DNA element. Sequence alignments, hidden Markov models (HMMs). For complete Eukaryote genomes. More. You can find data in Dfam in various ways. Analyze your DNA sequence for Dfam matches. Paste your DNA sequence here to find matching Dfam entries. This search will search against all Dfam models ( regardless of clade ) and using the trusted cut-off thresholds (stringent). You can set your own search parameters here.

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