Overview of SequenceServer Features

SequenceServer has many features that will accelarate your research,
allowing you to extract the most from your data.

Powerful BLAST Submission Interface

SequenceServer provides an easy-to-use and helpful interface. It auto-detects whether the input sequence is either nucleotide or amino acid. With the combination of input data and database type, SequenceServer selects only appropriate BLAST algorithms to use. This helps you to make mistake-free analysis of your data.

SequenceServer comes packaged with useful databases as default. These include NCBI nr/nt and UniProtKB/SwissProt databases, and genomic, transcriptomic and proteomic databases for several of the most commonly searched organisms (human, mouse, fruit fly and thale cress). This saves time, effort and database management.

Advanced Parameters of BLAST made easy with SequenceServer. There are many preset options and easy-to-use help directions.

East-to-Use Advanced Parameter Selection

SequenceServer gives you access to preset parameter options, enabling you to analyze different data types. Alternatively, you can have complete customization of parameters, with your parameter history saved for future use. This flexibility enables you to optimize your time and search sensitive.

Expansive BLAST Result Overview

SequenceServer goes beyond your standard BLAST results. A comprehensive overview of your search results is generated in an interactive and easy-to-manipulate format. Multiple different graphical representations of results allow you to visualize and interpret BLAST results. These graphs can be easily downloaded and are ideal for publication and presentation.

SequenceServer provides a range of functionality tools, allowing you to extract reports, alignments and FASTA files.

BLAST Result Overviews with SequenceServer help you extract the most value from your investigations.
DNA Visualizer with SequenceServer is useful for helping annotate plasmids, bacterial genomes and gene sequences.

Annotate and explore features with DNA Visualizer

SequenceServer provides a straightforward bacterial genome and plasmid annotation tool. This makes gene identification and exploration quick and easy. The interactive interface allows for customization of plots so you can focus in on the data that matters. Outputs for downstream analysis are easy to download.

BLAST to the NCBI Short Read Archive

SequenceServer enables you to search the NCBI Short Read Archive (SRA) with ease. This is a powerful way to explore a huge repository of data without the need for download times. SequenceServer allows you to download various formats including alignments, FASTA files of hits, and BLAST results output, which facilitates further downstream analysis.

SRA input BLAST with SequenceServer allows you to search publicly available sequence data for hits to your query.
CDD annotation of input query sequences with SequenceServer lets you see what functional domains your sequences possess.

Analysis of Conserved Domains

SequenceServer identifies possible functionality by annotating your query and BLAST hits using the Conserved Domain Database (CDD). This provides immediate help in the identification of possible orthologues and functional similarities during your BLAST searches. Graphical and text outputs are provided so that you can understand and analyze your results how you prefer.

Length Distribution of BLAST Hits

Length distribution and identity metrics of your hits help to identify similarities and differences between your query and the BLAST hits. For example, this query (a predicted gene product) is approximately twice as long as the sequences it is similar to.

Length distribution of BLAST hits is a great way to compare your query with the subject hits and understand differences between them.
Pairwise BLAST Alignments are useful for comparing sequence differences.

Pairwise BLAST Alignments

Visualization of pairwise BLAST alignments is a powerful means to quickly understand how your query aligns to hits. In combination with SequenceServer’s CDD annotation, this enables you to see what regions of your alignment might relate to important conservation and divergence.

It gives quick interpretations of your alignment, allowing you to detect and explore genomic features like inversions, insertions and deletions.

Circos-Style Visualization of BLAST Queries and Hits

Offering a compelling and intuitive representation of BLAST queries and hits. These plots are a great way of interpreting multiple hits simultaneously. They give information of the score (E-value), position and length of alignments. Interactive elements allow you to select the features you want to highlight.

Circos-style visualization of BLAST queries and hits help to interpret your results and can be used for publications.
BLAST Hits can fall in various places along your query sequence. This visualization helps you understand where aligned regions are positioned.

BLAST Hit Similarity Score

Get an overview of where alignment hits fall in relation to your query. BLAST hit sequences (shades of red) aligning to the query sequence (black). Darker color means stronger similarity (i.e., E-value).

Share your BLAST results with others

SequenceServer is excellent for team-based applications. Sharing your BLAST results is the easiest way to facilitate collaborative research, streamlining the process of analysis and mutual discovery in genomic studies. With annotation capabilities, you can use SequenceServer to record and archive your results for the whole team to be able to access.

Share your BLAST results with others so that you can build a network of knowledge.
BLAST History is a powerful user interface that allows you to keep records of all your searches and go back to them without computationally expensive reruns.

History of BLAST Searches

Never lose track of your research with SequenceServer’s automatic logging and retrieval. You will always be able to go back to your previous BLAST results. This ensures you can keep track of software parameters, datasets, queries and more, making your research robust and reproducible. This overview page of BLAST searches done by you and your team gives you access to all previous results.