BLAST analysis thoughts and advice

We're constantly thinking about how to improve and support genomic analyses.

The posts below include:

The interpretation of BLASTN results

Exploration and overview of BLASTN inputs and outputs. This covers the core concepts and metrics used with BLASTN

The interpretation of BLASTN results
Taxonomic restriction of BLAST searches

How to taxonomically restrict BLAST searches to achieve better results and refine your research questions

Taxonomic restriction of BLAST searches
The DNA Visualizer tool for feature exploration on SequenceServer

Detection and visualization of DNA features. An easy-to-use bacterial genome and plasmid annotation tool, with added visualisation tools.

The DNA Visualizer tool for feature exploration on SequenceServer
Generating guide RNAs and sequencing primers for CRISPR knockouts

How to use SequenceServer to design guide RNAs for CRISPR knockouts, assessing mutation sites and off-targetting

Generating guide RNAs and sequencing primers for CRISPR knockouts
Search Raw Reads from NCBI's SRA Database 🧬

How to search the SRA Database with SRA BLAST. Enabling massive screening of publically available data

Search Raw Reads from NCBI's SRA Database 🧬
Improvements to BLAST search in SequenceServer 3.0

Release notes for SequenceServer 3.0. This release includes new features, maintenance, bugfixes and minor improvements.

Improvements to BLAST search in SequenceServer 3.0
Comparing FASTA and FASTQ Sequence Formats

What are FASTA and FASTQ sequence formats, when are they used, and what kind of information do they contain.

Comparing FASTA and FASTQ Sequence Formats
Citation Guidelines for NCBI BLAST

It's important to cite BLAST and its related software and data sources in your publications.

Identifying conserved protein domains to understand gene function

Annotate proteins with the CDD Conserved Domain Database in SequenceServer. Improve your understanding of functional domains in your sequences

Identifying conserved protein domains to understand gene function
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We've started a referral scheme. Help your friends and earn cash!

BLASTN, TBLASTX, BLASTP, TBLASTN, BLASTX - which should I choose?

BLAST algorithm choice depends on what type of query sequence you're comparing to which type of database. It's critical to choose the correct one.

BLASTN, TBLASTX, BLASTP, TBLASTN, BLASTX - which should I choose?
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SequenceServer BLAST 2.2.0 release notes

Version 2.2.0 starts up much faster, and improves performance and usability with large queries

SequenceServer BLAST 2.2.0 release notes
Logging BLAST server access and genomic data download

Audit trails and access trails for BLAST database. Great for monitoring student engagement, and Configuring user access and databases for a SequenceServer Cloud BLAST server

Logging BLAST server access and genomic data download
Setting Up and Running a Custom BLAST Server: technical & logistical considerations

Appropriately leveraging powerful tools like BLAST is essential for success. Here, we walk through some of the things you need to think about when setting up and running a custom BLAST server.

Setting Up and Running a Custom BLAST Server: technical & logistical considerations
SequenceServer BLAST 2.1 release notes

Version 2.1 includes many new features and bugfixes, including Cloud Sharing, NCBI BLAST 2.14, backend improvements and improvements to architecture and robustness.

SequenceServer BLAST 2.1 release notes
Disentangling homology, orthology, paralogy and similarity with BLAST

We define what are orthologs, homologs and paralogs. Using examples and a case study (Tachykinin vs Neuro-peptide Y) we clarify how BLAST can help to elucidate relationships among genes.

Disentangling homology, orthology, paralogy and similarity with BLAST
Metabarcoding to identify organisms from environmental DNA (eDNA) with BLAST

BLAST can help identifying organism in an environmental sample using a metabarcoding approach

Metabarcoding to identify organisms from environmental DNA (eDNA) with BLAST
How BLAST E-values are calculated and what they mean

Here we take a look at the BLAST E-value and how it is used in BLAST

How BLAST E-values are calculated and what they mean
Identifying gene sequences in a new genome assembly using BLAST

BLAST can help us obtain the gene sequences from the genomes we are interested in

Identifying gene sequences in a new genome assembly using BLAST
Check PCR primer specificity using BLAST but without primer blast

Five things to do when checking primer specificity using BLAST. Make sure you get the best PCR results!

Check PCR primer specificity using BLAST but without primer blast
BLASTing Illumina reads in FASTQ format

BLAST is powerful, but not necessarily appropriate for analysis of FASTQ files

BLASTing Illumina reads in FASTQ format
BLAST in the cloud

Run BLAST analyses in the cloud to get results faster, or search on unpublished data.

BLAST in the cloud
Visualizing and interpreting BLAST alignments

SequenceServer incorporates four powerful visualizations that help researchers interpret BLAST alignment results.

Visualizing and interpreting BLAST alignments
Point and click BLAST server configuration

Configuring user access and databases for a SequenceServer Cloud BLAST server

Point and click BLAST server configuration
Sequence Search

Whether you are studying the genetic makeup of an organism or trying to identify potential targets for drug development, sequence searches can provide valuable insights and information.

Sequence Search