https://www.nist.gov/news-events/news/2016/09/nist-releases-new-family-standardized-genomes

Address of the bookmark: https://jimb.stanford.edu/giab/

Address of the bookmark: https://github.com/awslabs/autogluon

1. Understand the Landscape

Before diving into applications, take the time to understand the bioinformatics job market. Common roles include:

• Bioinformatics Analyst/Scientist: Focused on data analysis and interpretation.
• Computational Biologist: Combines computational techniques with biological research.
• Data Scientist in Genomics: Applies machine learning and statistical models to genomic data.
• Software Developer in Bioinformatics: Designs and develops tools and pipelines for biological research.

Familiarize yourself with the key industries hiring bioinformaticians, such as academia, biotech, pharmaceuticals, healthcare, and agriculture.

2. Build a Strong Foundation

Bioinformatics demands a diverse skill set. Ensure you have a solid foundation in the following areas:

• Programming Skills: Proficiency in Python, R, or Perl is often required. Familiarity with tools like Bash scripting and version control systems (e.g., Git) is a plus.
• Statistics and Data Analysis: Knowledge of statistical methods, machine learning, and data visualization is crucial.
• Biological Knowledge: Understanding genomics, transcriptomics, and proteomics will help you communicate effectively with biologists.
• Specialized Tools and Databases: Be comfortable using tools like BLAST, Bowtie, and databases like NCBI and Ensembl.

3. Create a Winning Resume and Portfolio

Highlight your technical skills, biological knowledge, and relevant experience. Tips for a standout application:

• Tailor your resume to each job, emphasizing skills mentioned in the job description.
• Showcase your experience with real-world datasets by linking to your GitHub profile or online portfolio.
• Include details of any publications, presentations, or significant projects.

4. Network Actively

Networking is often the key to discovering opportunities. Here’s how to build connections:

• Attend Conferences and Workshops: Events like ISMB or specialized bioinformatics workshops are great for meeting professionals.
• Engage Online: Join LinkedIn groups, participate in bioinformatics forums, and follow relevant hashtags on Twitter.
• Leverage Alumni Networks: Connect with alumni from your university who are working in the field.

5. Gain Relevant Experience

Experience is a major factor for hiring managers. Ways to enhance your profile include:

• Internships: Seek out internships in research labs or biotech companies.
• Collaborations: Volunteer to work on projects with professors or peers.
• Open Source Contributions: Participate in bioinformatics software development on platforms like GitHub.

6. Prepare for Interviews

Bioinformatics interviews often combine technical and behavioral questions. Prepare by:

• Reviewing Key Concepts: Refresh your knowledge of algorithms, sequence analysis, and statistical methods.
• Practicing Coding: Be ready to solve coding challenges or discuss code snippets.
• Understanding the Organization: Research their recent projects, publications, or products.
• Preparing Questions: Demonstrate interest by asking about their tools, workflows, or team structure.

7. Stay Resilient and Persistent

Job hunting can be a long process, but persistence pays off. Tips to keep moving forward:

• Keep improving your skills by taking online courses or certifications.
• Stay updated with advancements in bioinformatics by following journals and blogs.
• Apply to multiple positions and don’t get discouraged by rejections. Each application is a learning experience.

Closing Thoughts

Landing a bioinformatics job requires a mix of technical expertise, networking, and resilience. By understanding the market, showcasing your skills effectively, and continuously learning, you’ll be well on your way to a rewarding career in this dynamic field. Remember, the key to cracking the code is perseverance—stay curious, stay determined, and success will follow.

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

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

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

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/

The changes in nr preserve the taxonomic diversity of the entries in the database while reducing the number of titles for identical sequences. GenPept accessions are still accessible via www.ncbi.nlm.nih.gov/protein/$GENBANK_ACCESSION or the IPG website https://www.ncbi.nlm.nih.gov/ipg/.

The "Identical Proteins" link in the alignments section of the webBLAST results takes you to a full list of all accessions associated with a sequence.

For BLAST+ users downloading nr_v5: the database is now approximately 50% smaller, resulting in faster downloads and BLAST searches, and smaller disk space requirements. The database is downloadable at:  ftp://ftp.ncbi.nlm.nih.gov/blast/db/v5/

For BLAST+ there is a cleanup script to help you manage the transition to this smaller database. The script removes unused database volumes: ftp://ftp.ncbi.nlm.nih.gov/blast/temp/cleanup-blastdb-volumes.py

Here are the new rules on how we keep titles in nr_v5:

1.    We keep all refseq, swissprot, pir and PDB titles.

2.    We keep any GenPept titles with a TAXID that has not already been seen in the record.

3.    We keep at least five GenPept titles regardless of whether the TAXIDS have been seen before or not in this record.