Tag: Basic Local Alignment Search Tool (BLAST)

Remembering Mark Boguski

It is with much sadness that we recently learned of the passing of Mark Boguski, MD, PhD, a former Senior Investigator in the Computational Biology Branch at NCBI. Mark worked at the NCBI from 1989-2000 and made a lasting impression on the staff who are still with NCBI and who overlapped with his time here. Many of them have commented on social media about their personal interactions and fond memories of Mark.

Figure 1. Part of an alignment from a translating BLAST (blastx) search of a modified chicken translation factor sequence that Mark provided to Michael Crichton for The Lost World. Mark had edited the sequence by inserting DNA codons that BLAST translates to ‘MARK WAS HERE NIH’ thus leaving his autograph. Continue reading “Remembering Mark Boguski”

April 7 Webinar: Recent and upcoming enhancements to NCBI BLAST and Primer-BLAST services!

April 7 Webinar: Recent and upcoming enhancements to NCBI BLAST and Primer-BLAST services!

Join us on April 7, 2021 at 12PM eastern time to learn about new web BLAST and Primer-BLAST enhancements that improve your BLAST experience. You’ll also see a preview of some planned improvements to the databases that make it easier to find relevant matches.

Recent changes to web BLAST include added data columns on the descriptions table, so you can quickly find and sort your matches. Primer-BLAST now offers direct links from genome assembly pages, so you can easily select the specificity database. Primer-BLAST also now accepts multiple target templates making it easy to design primers that can amplify several similar sequences such as all splice variants of gene or the same target (16S, COI) from different strains or species.

  • Date and time: Wed, April 7, 2021 12:00 PM – 12:45 PM EDT
  • Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI webinars playlist on the NLM YouTube channel. You can learn about future webinars on the Webinars and Courses page.

March 10 Webinar: Where to find data for your research organism!

March 10 Webinar: Where to find data for your research organism!

Do you work with data from organisms outside the traditional set of model organisms? Join us on March 10, 2021 to learn how to use NCBI resources including NCBI’s Taxonomy and BLAST that can help you find information from your organism and closely related taxa. You will see an example that shows you how to retrieve and download gene sequences for a set of species, generate multiple sequence alignments, and design primers using Primer-Blast.

  • Date and time: Wed, March 10, 2021 12:00 PM – 12:45 PM EST
  • Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

The Protein Family Model resource is now available!

The new Protein Family Model resource  (Figure 1) provides a way for you to search across the evidence used by the NCBI annotation pipelines to name and classify proteins. You can find protein families by gene symbol, protein function, and many other terms. You have access to related proteins in the family and publications describing members. Protein Family Models includes protein profile hidden Markov models (HMMs) and BlastRules for prokaryotes, and conserved domain architectures for prokaryotes and eukaryotes. The HMMs in the collection include Pfam models, TIGRFAMs as well as models developed at NCBI either de novo, or from NCBI protein clusters.  Each of the BlastRules (PMCID: 5753331) consists of one or more model proteins of known biological function with BLAST identity and coverage cutoffs.  The conserved domain architectures are based on BLAST-compatible Position Specific Score Matrices  (PSSMs) that constitute the NCBI Conserved Domain database.Figure 1. Protein Family Model resource pages. Top panel.  Home page. Middle  panel, selected results summaries from a fielded search for the DnaK gene product (DnaK[Gene Symbol]). Bottom panel, a portion of an HMM record for DnaK derived from NCBI Protein Clusters (NF009946). The record also includes PubMed citations and HMMER analyses showing the RefSeq proteins named by this method.

Continue reading “The Protein Family Model resource is now available!”

Primer-BLAST now designs primers for a group of related sequences

Primer-BLAST now has a “Primers common for a group of sequences” submission tab that allows you to design primers for a group of highly similar sequences. For example, you may want test for expression of any transcript of gene rather than a specific splice variant, so you want to design primers to cover all transcript variants.  Or you may want to design primers that will amplify the same gene in closely related bacteria strains.  To find primers for a group of related sequences, Primer-BLAST aligns the longest sequence to the rest to find common regions. It uses these to limit the locations of primers. The longest sequence is also used as the representative template sequence in the results.  Figure 1 shows an example search for primers that will amplify all of the 15 splice variants for the human TP53 gene.

Figure 1. Primer-BLAST submission page and results for primers designed for the human TP53 transcripts. Top panel: The submission form with the “Primers common for a group of sequences” selected and the 15 RefSeq transcript accessions for TP53. Middle panel: The graphical results showing the longest sequence (NM_001126114.3) as the representative template, the locations of the primer pairs, and the alignment of the other template sequences. Bottom panel: An individual primer pair showing the locations on each of the template sequences.

Please try out this new feature and let us know what you think!

New BLAST default parameters and search limits coming in September

To provide a more efficient BLAST experience for everyone, we’re changing some parameters and limits on the web BLAST service on September 8, 2020. The new settings, listed below, will improve overall performance and make search times more consistent.

  1. The Expect Value Threshold default setting will be reduced to 0.05.
  2. The maximum number of target sequences (Max target sequences) limit will be no more than 5,000.
  3. The maximum allowed query length for nucleotide queries (blastn, blastx, and tblastx) will be 1,000,000 and 100,000 for protein queries (blastp and tblastn).

These changes will help keep the BLAST service running smoothly as the already very large databases continue to grow rapidly. If you have any questions or concerns, please email us at blast-help@ncbi.nlm.nih.gov

Download high-quality graphics from the NCBI Multiple Sequence Alignment Viewer (MSAV)

You can now download a publication-quality graphic images of  the alignment displayed in the NCBI Multiple Sequence Alignment Viewer (Figure 1). Load sequence alignments into the viewer from BLAST or COBALT results or upload alignment files directly. Once you have the the alignment set in the viewer, choose the “Printer-friendly PDF/SVG” option in the Download menu on the toolbar to save the image. The PDF and SVG files contain vector graphics suitable for presentation and publication. MSA_downloadFigure 1. The image download options in the MSAV. You can adjust the desired coordinate range and choose to download a PDF or SVG image. You can also preview the PDF download . Choose simplified color shading to improve compatibility with some graphics programs.

The downloaded image will show the coordinate range you requested and will include all the rows in the alignment.

Please contact us through the Feedback link on the MSA Viewer or write to the NCBI Help Desk to provide feedback and let us know how we can make the NCBI Multiple Sequence Viewer work better for you.

A new version of IgBLAST (1.16.0) is here!

We’ve released a new version (1.16.0) of IgBLAST , the popular NCBI package for classifying and analyzing immunoglobulin (IG) and T cell receptor (TCR) variable domain sequences. Version 1.16.0 has three new improvements.

  1. Added the ability to extend the J gene alignment at 3’ the end of the region (Figure 1). This allows you to view the unaligned bases that otherwise would not be included because of low sequence similarity. IgBLAST_options

Figure 1. The new “extend alignment at the 3′ end” option on the IgBLAST web form. The command line option is ‘-extend_align3end’. Continue reading “A new version of IgBLAST (1.16.0) is here!”

Recalculation of prokaryotic reference and representative genome assemblies

We have updated the collection of representative and reference assemblies for Bacteria and Archaea to better reflect the taxonomic breadth of the prokaryotes in RefSeq.  We chose the 11,478 representative assemblies in the new collection from the 180,000+ prokaryotic assemblies in RefSeq today.  We have selected one representative or reference assembly for every species based on several criteria including contiguity, completeness and whether the assembly is from type material.  We have also updated the reference and representative microbial Blast database to reflect these changes. This reference and representative set will be updated three times a year to reflect changes in RefSeq.  In addition, as we announced on Feb 14, we have reduced the number of reference genome assemblies — the subset of representative assemblies with annotation provided by outside experts —  to 15. See the list in our previous post .  We have re-annotated the 104 assemblies that are no longer reference with or Prokaryotic Genome Annotations Pipel (PGAP).

New ribosomal RNA BLAST databases available on the web BLAST service and for download

We have a curated set of ribosomal RNA (rRNA)  reference sequences (Targeted Loci) with verifiable organism sources and current names. This set is critical for correctly identifying and classifying prokaryotic (bacteria and archaea) and fungal samples (Table 1). To provide easy access to these sequences, we recently added a separate rRNA/ITS databases section on the nucleotide BLAST page for these targeted sequences that makes it convenient to quickly identify source organisms (Figure 1)

Database BioProjects Sequences
16S ribosomal RNA (Bacteria and Archaea) PRJNA33317 , PRJNA33175

 

20,845
18S ribosomal RNA sequences (SSU) from Fungi type and reference material PRJNA39195 2,337
28S ribosomal RNA sequences (LSU) from Fungi type and reference material PRJNA51803 5,185
Internal transcribed spacer region (ITS) from Fungi and Oomycete type and reference material PRJNA177353, PRJNA362621

 

10,874

Table 1.  NCBI curated targeted rRNA sequences now available as BLAST databases. Continue reading “New ribosomal RNA BLAST databases available on the web BLAST service and for download”