ftp://ftp.ncbi.nih.gov/genomes/

https://hgdownload.soe.ucsc.edu/downloads.html

Address of the bookmark: ftp://ftp.ncbi.nih.gov/genomes/

Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results.

Genome Workbench is built on the NCBI C++ ToolKit and uses cross-platform APIs for graphics. It runs on your local machine, and is available for Windows 2000/XP, Linux, MacOS X, and various flavors of Unix.

NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. Genome Workbench was developed entirely in-house at NCBI and makes use of the NCBI C++ ToolKit. The C++ ToolKit provides a convenient and flexible cross-platform API for managing system internals, database connections, network sockets, and the NCBI data model. In addition, the C++ ToolKit provides the Object Manager, which abstracts handling of sequences and sequence-related objects.

 New Features in Genome Workbench 2.7.15

• Multiple Alignment View: implemented adaptive feature display when zooming in
• Active Objects Inspector replaces Selection Inspector. New View should offer an improved selection context examination. See Using Active Objects Inspector tutorial for more details.
• Binary packages for Linux OpenSUSE 13.1 are now available

Bug Fixes and Improvements in Genome Workbench 2.7.15

• Fixed major issue with OpenGL overlay/scrolling. Could cause crashes or view scrolling irregularities
• Multiple Pane View: fixed crash on loading BLAST results
• Graphical Sequence View: fixed crash on zooming in and out, related to SNP track
• Graphical Sequence View: fixed Go To Position dialog to give better diagnostics in case of a user error
• Graphical Sequence View: PDF export fixed rendering of Markers with commas in the name
• Text View / Flat File: fixed Mac OS rendering issues
• Text View / Flat File: performance optimization, extended capabilities of real-time rendering of molecules to tens of thousands
• File Import: optimization improvement to speed up load of files containing multiple project items
• File Import: remapping stage now shows accession.version and description of molecules, instead of plain GI numbers
• Mac OS: improved tooltips for toolbar buttons
• Phylogenetic Tree Builder Tool: improved diagnostics of errors
• Multiple Alignment View: optimizations to avoid main GUI freezes
• Open Dialog: removed duplicate elements in table of genomes (load Genome)
• PDF export: fixed issue with XREF table errors
• Tree View: fixed issues with showing Force Layout progress on Mac OS
• Tree View: PDF export fixed issues for showing labels of collapsed nodes
• Tree View: added an option to stop layout
• Tree View: broadcasting mechanism fixed not to accumulate selected nodes

Reference:

NCBI news

http://www.ncbi.nlm.nih.gov/tools/gbench/

More at http://www.ncbi.nlm.nih.gov/genome/tools/remap

API http://www.ncbi.nlm.nih.gov/genome/tools/remap/docs/api

Address of the bookmark: http://www.ncbi.nlm.nih.gov/genome/tools/remap

MutaBind guides you through this process, step by step, starting with selecting a protein complex and inputting PDB code or uploading PDB files. You can also retrieve results with a job ID number, view help documents, and review the MutaBind method and references.

More at http://www.ncbi.nlm.nih.gov/projects/mutabind/index.fcgi/

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

NCBI has developed an automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. The first version of NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP; see Pubmed Article) developed in 2005 has been replaced with an upgraded version that is capable of processing a larger data volume. You can find a more detailed description of the new version of the pipeline in NCBI Handbook chapter. NCBI's annotation pipeline depends on several internal databases and is not currently available for download or use outside of the NCBI environment.

https://www.ncbi.nlm.nih.gov/genome/annotation_prok/

Address of the bookmark: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/

As mentioned before, working with BLAST+ in Docker and the cloud has several advantages:

• Docker manages installation and maintenance of the BLAST programs and databases.
• Docker makes it is easier to integrate BLAST with other tools in your pipelines.
• NCBI BLAST databases are pre-loaded now on the both the Google Cloud and Amazon Cloud, providing fast access.

You can also use the BLAST+ Docker image on any Docker-enabled platform, such as another cloud platform or on your local computer.

See the  BLAST+ in the Cloud and  database information documentation to get started.

If you have any questions, please email us at blast-help@ncbi.nlm.nih.gov

Source:Dave Arndt

More at http://www.ncbi.nlm.nih.gov/news/06-16-2015-blast-plus-update/?

More at http://sequenceserver.com.

Address of the bookmark: https://github.com/wurmlab/sequenceserver

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