Updates to the Conserved Domain Database include:

• Position-specific score matrices (PSSMs) have been recomputed for many models in CDD, and frequency tables have been added to the PSSMs;

• The search databases distributed as part of this release can now be used with the more recent versions of RPS-BLAST (BLAST release 2.2.28 and up) using composition-based scoring. This abolishes the need to mask out compositionally biased regions in query sequences;

• Domain annotation displays in CD-Search, BATCH CD-Search, and other services now all use a uniform display style. A new display option in CD-Search and BATCH CD-Search provides “standard” results, in addition to “concise” and “full” results. “Standard” results will provide, for each region on the query sequence, the best0-scoring domain model (if any) from each of CDD’s database providers (Pfam, SMART, COG, TIGRFAMs, Protein Clusters, and the NCBI in-house curation project), but will suppress redundancy from within a single provider's results list.

You can access CDD at the Conserved Domains homepage and find updated content on the CDD FTP site.

Reference:

NCBI Website

More at http://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0/index.fcgi/browse/

Address of the bookmark: http://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0/index.fcgi/browse/

For example, you can run a search in Assembly and use check boxes (see left side of screenshot below) to refine the set of genome assemblies of interest. Then, just open the “Download assemblies” menu, choose the source database (GenBank or RefSeq), choose the file type, and start the download. An archive file will be saved to your computer that can be expanded into a folder containing your selected genome data files.

More at https://ncbiinsights.ncbi.nlm.nih.gov/2017/05/08/genome-data-download-made-easy/

    1. Support for the new FWR4 annotation feature in the AIRR format, both in standard format and in the AIRR alignment format.

    2. The previous “-penalty” parameter was renamed as -V_penalty to be consistent with other IgBLAST penalty options.

    3. Restored constant internal BLAST search parameters for domain annotation (i.e., FWR/CDR) such that this process is not influenced by user parameters.

    4. Corrected FWR/CDR annotations for certain mouse VK and rat VH germline genes. 

IgBLAST 1.15.0 is available for download from the BLAST FTP area. See the the new manual on GitHub for information about setting up and running IgBLAST.

 If you have any questions or concerns, please contact blast-help@ncbi.nlm.nih.gov

Address of the bookmark: https://github.com/reubwn/collinearity

java -Xmx8g -jar GenomeAnalysisTK.jar \
-T VariantsToTable \
-R reference.fa \
-V reference_genomes_GT.vcf \
-F CHROM -F POS -F REF -F ALT -GF GT \
-o reference_genomes_GT.table
multiple_sample.vcf should also be converted to multiple_sample_GT.table using this approach.

Features

• An amazing real-time web framework, allowing you to easily grow single file prototypes into well-structured MVC web applications.
  • Powerful out of the box with RESTful routes, plugins, commands, Perl-ish templates, content negotiation, session management, form validation, testing framework, static file server, CGI/PSGI detection, first class Unicode support and much more for you to discover.
• A powerful web development toolkit, that you can use for all kinds of applications, independently of the web framework.
  • Full stack HTTP and WebSocket client/server implementation with IPv6, TLS, SNI, IDNA, HTTP/SOCKS5 proxy, UNIX domain socket, Comet (long polling), Promises/A+, keep-alive, connection pooling, timeout, cookie, multipart and gzip compression support.
  • Built-in non-blocking I/O web server, supporting multiple event loops as well as optional pre-forking and hot deployment, perfect for building highly scalable web services.
  • JSON and HTML/XML parser with CSS selector support.
• Very clean, portable and object-oriented pure-Perl API with no hidden magic and no requirements besides Perl 5.24.0 (versions as old as 5.10.1 can be used too, but may require additional CPAN modules to be installed)
• Fresh code based upon years of experience developing Catalyst, free and open source.
• Hundreds of 3rd party extensions and high quality spin-off projects like the Minion job queue.

http://mojolicious.org/

Address of the bookmark: http://mojolicious.org/

Address of the bookmark: http://kobas.cbi.pku.edu.cn/

# plumber.R

#* Echo back the input
#* @param msg The message to echo
#* @get /echo
function(msg=""){
  list(msg = paste0("The message is: '", msg, "'"))
}

#* Plot a histogram
#* @png
#* @get /plot
function(){
  rand <- rnorm(100)
  hist(rand)
}

#* Return the sum of two numbers
#* @param a The first number to add
#* @param b The second number to add
#* @post /sum
function(a, b){
  as.numeric(a) + as.numeric(b)
}

Address of the bookmark: https://www.rplumber.io/