Difference between revisions of "Biocluster Mirrors"

From Carl R. Woese Institute for Genomic Biology - University of Illinois Urbana-Champaign
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{| style="width: 900px;  margin: 0 auto" class="wikitable" border="1" cellpadding="1" cellspacing="1"
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{| style='margin: 0 auto' class='wikitable' border='1' cellpadding='1' cellspacing='1'
 
|-
 
|-
! Data Set
+
!Application
! Website
+
!Installed Versions
! Description
+
!Description
! Update Schedule
 
! File System Path
 
 
|-
 
|-
| Bioconductor
+
|[https://card.mcmaster.ca card-prevalence]
| [http://www.bioconductor.org/ http://www.bioconductor.org/]
+
|3.0.6
 +
|November 2019 release - 85 pathogens, 116914 resistomes, and 182532 AMR allele sequences based on sequence data acquired from NCBI on July 31, 2019, analyzed using RGI 5.0.0 (DIAMOND homolog detection) and CARD 3.0.7. Includes pre-compiled k-mer classifier data for pathogen-of-origin prediction.
 +
|-
 +
|[http://huttenhower.sph.harvard.edu/humann2 chocophlan]
 +
|0.1.1
 
|
 
|
| Weekly
 
| /home/mirrors/no_backup/R/bioconductor/
 
 
|-
 
|-
| Cran
+
|[http://www.molgen.ua.ac.be/bioinfo/projects/clusterblast/clusterblast.htm clusterblast]
| [http://cran.r-project.org/ http://cran.r-project.org/]
+
|20170105
 
|
 
|
| Weekly
 
| /home/mirrors/no_backup/R/cran/
 
 
|-
 
|-
| BLAST DBs
+
|[https://www.ebi.ac.uk/ena ena]
| [[Ftp:ftp://ftp.ncbi.nlm.nih.gov/blast/db|ftp.ncbi.nlm.nih.gov/blast/db]]
+
|Release_130
 +
|The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing.
 +
|-
 +
|[https://software.broadinstitute.org/gatk/download/bundle gatkbundle]
 +
|20191118
 +
|he GATK resource bundle is a collection of standard files for working with human resequencing data with the GATK. We provide several versions of the bundle corresponding to the various reference builds,
 +
|-
 +
|[https://www.ncbi.nlm.nih.gov/genbank/ genbank]
 +
|238
 +
|GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences
 +
|-
 +
|[https://www.ebi.ac.uk/interpro/ interpro]
 +
|68.0
 +
|InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.
 +
|-
 +
|[ftp://ftp.ncbi.nlm.nih.gov/blast/db/ ncbi-blastdb]
 +
|20170702<br>20180404<br>20190320<br>20190808
 
|
 
|
| Weekly
 
| /home/mirrors/NCBI/BLAST_DBS/
 
 
|-
 
|-
| Uniprot
+
|[https://pfam.xfam.org/ pfam]
| [[Ftp:ftp://ftp.uniprot.org/pub/databases/uniprot|ftp.uniprot.org/pub/databases/uniprot]]
+
|32.0
|
+
|The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)
| Monthly
+
|-
| /home/mirrors/uniprot/
+
|[https://www.uniprot.org/ uniprot]
 +
|2018_04
 +
|The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
 
|}
 
|}

Latest revision as of 12:11, 9 December 2020

Application Installed Versions Description
card-prevalence 3.0.6 November 2019 release - 85 pathogens, 116914 resistomes, and 182532 AMR allele sequences based on sequence data acquired from NCBI on July 31, 2019, analyzed using RGI 5.0.0 (DIAMOND homolog detection) and CARD 3.0.7. Includes pre-compiled k-mer classifier data for pathogen-of-origin prediction.
chocophlan 0.1.1
clusterblast 20170105
ena Release_130 The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing.
gatkbundle 20191118 he GATK resource bundle is a collection of standard files for working with human resequencing data with the GATK. We provide several versions of the bundle corresponding to the various reference builds,
genbank 238 GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences
interpro 68.0 InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.
ncbi-blastdb 20170702
20180404
20190320
20190808
pfam 32.0 The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)
uniprot 2018_04 The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.