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www.cosmoss.org - The Physcomitrella patenscomputational biology resource

www.cosmoss.org - The Physcomitrella patens computational biology resource

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University of Freiburg Plant Biotechnology

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www.cosmoss.org - The Physcomitrella patenscomputational biology resource | cosmoss.org Reviews
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www.cosmoss.org - The Physcomitrella patens computational biology resource
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1 Physcomitrella
2 Physcomitrella patens
3 moss
4 moos
5 Blasenmützenmoos
6 bioinformatics
7 bioinformatik
8 EST
9 cluster
10 contig
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cosmoss org,plant biotechnology,about physcomitrella,transcriptome,blast,sequence retrieval,keyword search,utr repeats,plantapdb,genonaut,genome,splice site prediction,ecotypes,genetic map,physcome project wiki,mirna,supplementary trees,downloads,tools
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www.cosmoss.org - The Physcomitrella patenscomputational biology resource | cosmoss.org Reviews

https://cosmoss.org

www.cosmoss.org - The Physcomitrella patens computational biology resource

INTERNAL PAGES

cosmoss.org cosmoss.org
1

Documentation

http://www.cosmoss.org/doc.content

Genome Browser (V1.6). Genome Browser (V3.3). The cosmoss mailing lists. Cosmoss Info / About. The nr (non redundant) dataset is based on the ppp dataset (see below). However, each cluster is represented by the longest sequence it contains only. This is similar to the NCBI's unique unigene. Approach. In theory, the nr set represents all genes present in the ppp dataset as well. Nucleic acid database. This dataset is based on the ppp nr. This database is a cleaned up version of the raw EST input data....

2

Cosmoss accounts - PhyscomeProjectWiki

http://www.cosmoss.org/physcome_project/wiki/Cosmoss_accounts

Cosmoss.org extended services and user accounts. Everyone is invited to register! Please contact helpdesk-cosmoss@uhura.biologie.uni-freiburg.de. The general use of the services of cosmoss.org are free of charge and open to everyone. We offer additional and extended services to registered users (e.g. additional BLAST databases, batch BLAST jobs, BLAST2CSV service, custom BLAST databases). Usage of these extended services is free to academia only. 250 /year per account. Account free of charge. To send req...

3

Main Page - PhyscomeProjectWiki

http://www.cosmoss.org/physcome_project/wiki

Welcome to the Physcome Project and cosmoss.org Wiki! These pages are meant to organize, document and discuss the efforts around the assembly and annotation of the Physcomitrella patens. Furthermore, it is used to document and organize the cosmoss.org community resources. For more information on Physcomitrella. Systematics see this Physcomitrella. The full taxonomic name is Physcomitrella patens. Hedw) Bruch and Schimp. see the Missouri Botanical Garden Tropicos database. The Third The cossmoss.org P...

4

PlanTAPDB - Retrieval

http://www.cosmoss.org/bm/plantapdb

Genome Browser (V1.6). Genome Browser (V3.3). The cosmoss mailing lists. Cosmoss Info / About. Welcome to PlanTAPDB version 1.0. Gene clusters were built by using PSI-BLAST searches and subsequent filtering and clustering steps followed by a comprehensive manual annotation procedure. Phylogenies were created in an automated way for all families using a combination of distance and maximum likelihood methods. The TAP families are listed below, grouped according to their functional category. BSD domain doma...

5

Downloads - PhyscomeProjectWiki

http://www.cosmoss.org/physcome_project/wiki/Downloads

Genome assembly and annotation V1.2. Downloads genome annotation version 1.6. Functional annotation - genonaut dumps. Latest Release 2012.3. Master branch - Nightly-build. Mapping to old annotation releases. Genome assembly and annotation V1.2. If you use this data, please cite: Lang, D., A.D. Zimmer, S.A. Rensing, R. Reski (2008): Exploring plant biodiversity: the Physcomitrella genome and beyond. Trends in Plant Science 13, 542-549. Genomic scaffolds based on the V1.0 JGI assembly. 32,275 gene structur...

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LINKS TO THIS WEBSITE

ackbar.dmz-biologie.uni-freiburg.de ackbar.dmz-biologie.uni-freiburg.de

Plant Biotechnology - The Ralf Reski Page

http://ackbar.dmz-biologie.uni-freiburg.de/navigation.html

cyclamen-est.de cyclamen-est.de

BLAST against the Cyclamen EST database

http://www.cyclamen-est.de/BLAST

BLAST against the Cyclamen EST database. Cp (01/05 V1.0 annotated). Cp chip (1,222 Cyclamen chip transcripts). Cp orfpep (01/05 redundant). This service is hosted by www.cosmoss.org.

archive.plants.ensembl.org archive.plants.ensembl.org

Physcomitrella patens - Ensembl Genomes

http://archive.plants.ensembl.org/Physcomitrella_patens/Info/Index

Are non-vascular plants that appeared very early in the fossil record, soon after the transition of plants to terrestrial environments. The. More information and statistics. More information and statistics. Display your data in Ensembl Plants. What can I find? Protein-coding and non-coding genes, splice variants, cDNA and protein sequences, non-coding RNAs. More about this genebuild. Download genes, cDNAs, ncRNA, proteins - FASTA. What can I find? More about comparative analyses. EMBL-EBI Terms of use.

cyclamen-est.de cyclamen-est.de

Sequence Retrieval documentation - www.cyclamen-est.de

http://www.cyclamen-est.de/retrieval-doc.html

Sequence Retrieval documentation - www.cyclamen-est.de. Sequence Retrieval User Manual. Retrieving sequences from a BLAST result. The main retrieval dialog. Retrieving sequences based on accession numbers. The sequence overview graphic. The sequence and annotation data. Using retrieval from scripts. 11 Using sequence retrieval. The main purpose of the sequence retrieval is to retrieve and display a given set of sequences. There are three distinct use cases:. Retrieving sequences from a BLAST result.

my-plant.org my-plant.org

Mosses | My-Plant.org

https://my-plant.org/clade/mosses

Phylogenetically Based Social Network for the Plant Sciences. Moss social network group. Include posts from subclades:. The latest in the feed. SO BE FREE 16 was held in the northern Sierra Nevada March 23 - 26, 2011. Posted by Brent Mishler, Apr 08, 2011. Http:/ ucjeps.berkeley.edu/bryolab/So Be Free 11.html. WHS workshop on phylogenetic methods, 2011. Posted by Efrain De Luna, Jan 25, 2011. This course will be possible thanks to the support from INECOL and WHS. Read more ». Visit his gallery at:. Most ...

cyclamen-est.de cyclamen-est.de

BLAST documentation - www.cyclamen-est.de

http://www.cyclamen-est.de/doc.html

BLAST documentation - www.cyclamen-est.de. The maximum number of detailed alignments to be shown (default: 50). The database you want to search (default: ppp nr). See details on the about page. Ppp nr (na): [default]. Clustered and assembled public Physcomitrella patens. EST sequences as of 29.01.2004 (102,932), non-redundant representation (only the longest sequence from each cluster): 22,182. Clustered and assembled public Physcomitrella patens. Filtered public Physcomitrella patens. Determines whether...

bezanillalab.com bezanillalab.com

Bezanilla Lab

http://www.bezanillalab.com/mossmethods.html

Moss should be propagated weekly. A detailed explanation can be found in the moss manual. By removing the cell walls from moss tissue, it is possible to generate a suspension of single cells called protoplasts. Moss protoplasts can be transformed with DNA and then regenerated into whole plants. For details on this procedure, please refer to the moss manual. Complementation studies provide validation of loss-of-function studies and mechanistic insights into gene function. By targeting untranslated reg...

ensembl.gramene.org ensembl.gramene.org

Physcomitrella patens - Ensembl Genomes

http://ensembl.gramene.org/Physcomitrella_patens/Info/Index

Are non-vascular plants that appeared very early in the fossil record, soon after the transition of plants to terrestrial environments. The. More information and statistics. More information and statistics. Display your data in Ensembl Plants. What can I find? Protein-coding and non-coding genes, splice variants, cDNA and protein sequences, non-coding RNAs. More about this genebuild. Download genes, cDNAs, ncRNA, proteins - FASTA. Update your old Ensembl IDs. What can I find? Genomic alignments [3] [ Show.

frisys.biologie.uni-freiburg.de frisys.biologie.uni-freiburg.de

FRISYS - Freiburg Initiative for Systems Biology

http://www.frisys.biologie.uni-freiburg.de/tools.html

FRISYS algorithms, software tools and databases. Http:/ www.potterswheel.de/. Freiburg RNA Tools: Prediction of RNA-RNA interactions, exact RNA matching and RNA alignments. Http:/ rna.informatik.uni-freiburg.de:8080/index.jsp. RNA software and server. Http:/ www.bioinf.uni-freiburg.de/Software/. Transcriptome of the model cyanobacterium Synechocystis sp. PCC6803. Http:/ www.cyanolab.de/Supplementary.html. The the moss computational biology toolbox. Http:/ www.cosmoss.org/.

cyclamen-est.de cyclamen-est.de

Sequence Retrieval

http://www.cyclamen-est.de/retrieval

Cp (01/05 V1.0 annotated). Cp chip (1,222 Cyclamen chip transcripts). Cp orfpep (01/05 redundant). You can retrieve multiple sequences by providing their accession numbers as a comma- or space-separated list in the textfield above. Or you provide them in a file with one accession number per line. This service is hosted by www.cosmoss.org.

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www.cosmoss.org - The Physcomitrella patenscomputational biology resource

Genome Browser (V1.6). Genome Browser (V3.3). The cosmoss mailing lists. Cosmoss Info / About. The pre-release of the new moss genome annotation V3.3. Is online. Browse now! Welcome to the moss computational biology toolbox. This site provides computational biology resources that are related to the genome/transcriptome of the model plant Physcomitrella patens. Has been sequenced by whole-genome shotgun at the JGI ( why? The version 1.1. Service against the assembled transcriptome and the genome.

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