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Cosmoss specifications

Information


Unique identifier OMICS_15229
Name Cosmoss
Interface Web user interface
Restrictions to use None
Input data Sequence
Input format TXT, FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Stefan Rensing

Publication for Cosmoss

Cosmoss citations

 (32)
library_books

Alternate Modes of Photosynthate Transport in the Alternating Generations of Physcomitrella patens

2017
Front Plant Sci
PMCID: 5693889
PMID: 29181017
DOI: 10.3389/fpls.2017.01956

[…] The amino acid sequences for H+PPase and SUS orthologs in P. patens were identified by BlastP in www.cosmoss.org or www.gramene.org, using the reference sequences from A. thaliana, Vigna radiata, and Oryza sativa. The amino acid sequences were first aligned using MUSCLE built-into the MEGA5 software, […]

library_books

Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens

2017
Sci Rep
PMCID: 5457400
PMID: 28578384
DOI: 10.1038/s41598-017-02970-z

[…] f exon per million fragments mapped (FPKM); only genes with FPKM ≥ 0.2 were used for further analysis. To define the functions of the identified genes, we used moss genome annotation v1.6 (http://www.cosmoss.org) and BLAST search against annotated A. thaliana sequences.To define the ratio of transcripts spliced by U2 and U12 spliceosomes, we evaluated conserved splice signals in the exon–intron ju […]

call_split

Selfing in Haploid Plants and Efficacy of Selection: Codon Usage Bias in the Model Moss Physcomitrella patens

2017
Genome Biol Evol
PMCID: 5507605
PMID: 28549175
DOI: 10.1093/gbe/evx098
call_split See protocol

[…] filtered the raw data sets using trimmomatic (; -phred33 ILLUMINACLIP: Hiseq_.fa:2:30:10:8:true LEADING:9 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36) and mapped reads to the P. patens v1.6 (https://www.cosmoss.org/physcome_project/wiki/Downloads; last accessed May 1, 2017) genome using tophat2 (). We used all these RNA-seq data to refine gene model annotations of the P. patens v1.6 gff files (link s […]

call_split

A Lin28 homologue reprograms differentiated cells to stem cells in the moss Physcomitrella patens

2017
Nat Commun
PMCID: 5290140
PMID: 28128346
DOI: 10.1038/ncomms14242
call_split See protocol

[…] sormidium/kf_download.htm Pinus taeda assembly 1.01 annotation v2 http://dendrome.ucdavis.edu/ftp/Genome_Data/genome/pinerefseq/Pita/v1.01/Pita_Annotation_v2/, and P. patens v1.6 data set https://www.cosmoss.org/physcome_project/linked_stuff/Annotation/V1.6/P.patens.V6_filtered_cosmoss_proteins.fas.gz, were performed using PpCSP1 through http://moss.nibb.ac.jp/cgi-bin/blast-nr-Kfl. According to BL […]

library_books

The Transcriptional Response to DNA Double Strand Breaks in Physcomitrella patens

2016
PLoS One
PMCID: 4990234
PMID: 27537368
DOI: 10.1371/journal.pone.0161204

[…] The transcriptome analysis was performed using Version 1.2.1 of the P. patens genome and filtered cleaned gene models, which were obtained from http://www.cosmoss.org/. The Illumina reads were mapped to the P. patens genome using the program TopHat [, ]. When mapping the reads to the P. patens genome, TopHat was run using default settings and a list of […]

call_split

Kinesin 2 and kinesin 9 have atypical functions during ciliogenesis in the male gametophyte of Marsilea vestita

2016
BMC Cell Biol
PMCID: 4947347
PMID: 27421907
DOI: 10.1186/s12860-016-0107-7
call_split See protocol

[…] Sequences for previously analyzed kinesin-2 and kinesin-9 family members were obtained using NCBI [], Phytozome [], and Cosmoss [] databases. The motor domain from each sequence was identified using the NCBI Conserved Domain Database [] and isolated for analysis. Phylogenetic trees for kinesin-2 and kinesin-9 were buil […]

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Cosmoss institution(s)
Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany

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