Sequence Editing Software and Annotation Tools

SEQUENCE EDITING AND ANNOTATION

Comprehensive sequence editing software, including automated sequence creation and batch editing capabilities.

Use SeqBuilder Pro for comprehensive sequence editing and annotation in one easy-to-use application!

Sequence editing is such a primary part of molecular biology research that it may seem like any sequence editing software will do. But ultimately, the convenience and capabilities of the tools you choose do matter. SeqBuilder Pro not only offers all of the expected functionality of a sequence editor: the ability to change nucleotides and amino acids, translate, reverse complement, add features, identify ORFs, and introduce restriction sites, but additionally provides automated batch editing tools so that you can seamlessly create and edit groups of sequences simultaneously, allowing you to accomplish your sequence editing goals faster. The live, interactive views in SeqBuilder Pro make it effortless to edit and annotate your sequences, customize your features and create plasmid maps. Our sequence editing software is also integrated with NCBI databases, making it easy to access and search online databases. The tools you use matter. Use SeqBuilder Pro to have access to everything you need for sequence editing and annotation in one easy-to-use application.

Sequence editing and annotation in 4 simple steps

Step 1

Open any sequence file

Step 2

Edit your sequence

Step 3

Add, edit, and customize annotations

Step 4

Use batch editing capabilities to edit or create groups of sequences

Learn more about our Sequence Editing Software

Resources | Tutorials | FAQs | Citations | User Guide

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Resources

Please see our resources below for more information on our sequence editing and sequence annotation tools.

Learn SeqBuilder Pro Workflows

Watch Webinar

Master Our Foundation Application, SeqBuilder Pro

Watch Webinar

SeqBuilder Pro FAQ: Answers to Your Webinar Questions

Read Blog Post

Automated Plasmid Annotation Webinar

Watch Webinar

Cloning and Primer Design Workflows Webinar

Watch Webinar

Enhanced Sequence Analysis for Today’s Molecular Biologist

Watch Webinar

Creating the curated feature library for accurate vector auto-annotation

Read Blog Post

Lasergene Molecular Biology Overview

View Document

Tutorials

Watch one of our videos or check out one of our written tutorials to learn more about sequence editing and sequence annotation in SeqBuilder Pro.

Automated Plasmid Annotation

This video demonstrates the plasmid auto-annotation functionality in SeqBuilder Pro which allows you to accurately and automatically annotate your sequences using a carefully curated database of features. Simply select your sequences and SeqBuilder Pro will provide you with a list of matched features for your consideration.

Translating sequences with SeqBuilder Pro

SeqBuilder Pro lets you show translations for all of a DNA/RNA sequence, or just a portion of it. It also lets you make a new protein sequence by translating one nucleotide sequence or thousands of them simultaneously. Learn how to do all of these tasks in this video.

Preparing a Map for Presentation in SeqBuilder

This video shows you how to rearrange and edit the annotations that are displayed on your plasmid map to prepare it for publication.

FAQs

What file types can I import for sequence editing?

SeqBuilder Pro supports virtually any type of sequence file, including FASTA, ABI, and GenBank formats, and easily imports files from Vector NTI, SnapGene, and Geneious. For a full list of supported file types, see our File Formats resource.

How can I control which restriction enzymes are displayed on my sequence?

The Enzymes panel lets you control which enzymes are displayed on your sequence. You can choose to apply groups of enzymes based on the frequency of cuts, type or class, site complexity, overhang compatibility, or an intersection of any of these groups. You can also choose to show/hide individual enzymes from the Enzymes panel by simply checking or un-checking the box next to its name.

How do I add annotations to my sequence?

The sequence annotation tools in SeqBuilder Pro make it easy annotate your sequence. Simply select the range of sequence for your annotation and do one of the following:

Choose Features>New…

The sequence annotation tools in SeqBuilder Pro make it easy annotate your sequence. Simply select the range of sequence for your annotation and do one of the following:

Choose Features>New Feature to create a new misc_feature.
Choose Features>New Feature with Translation to create a new CDS feature with a /translation qualifier attached to it.

The feature type and rendering for any feature can be changed at any point from the Features view.

Can I create reverse complements of multiple sequences simultaneously?

Yes. To reverse complement one or more sequences, choose Tools > Batch Reverse Complement. In the resulting window, add the sequences you wish to reverse complement into the Sequences folder, then click Run. The reverse complemented sequences will be displayed in the Results folder.

Can I create reverse complements of multiple sequences simultaneously?

Can I create translations of multiple sequences simultaneously?

Yes. To translate one or more nucleic acid sequences into protein sequences, choose Tools > Batch Translate. In the resulting window, add the sequences you wish to translate into the Sequences folder. Choose the reading frame and genetic code to be used for translation, then click Run. The tranlated sequences will be displayed in the Results folder.

How do I join multiple sequences together into a single sequence?

The sequence editing tools in SeqBuilder Pro make it easy to join two or more sequences end-to-end. To do this, choose Tools>Concatenate. In the resulting window, add the sequences you wish to join into the Sequences folder. Select the output file format, then click Run. The new concatenated sequence will be displayed in the Results folder.

What file types are supported for exporting my edited sequence file?

SeqBuilder Pro supports the export of many different file types, including EMBL, FASTA, and GenBank formats. For a full list of supported file types, see our File Formats resource.

Can I export an image of my sequence for publication?

Yes. Our sequence editing software allows you to save the sequence view, circular map view, or linear map view as an image for publication. First, make sure the view you want to export is active, then select Edit>Copy as Picture. This copies the image to your clipboard to be pasted into another application. When pasting the copied picture into a Microsoft Office application, we recommend using Edit>Paste Special and selecting Picture (Enhanced Metafile).

Citations

Temporal and Spatial Expression of Arabidopsis Gene Homologs Control Daylength Adaptation and Bulb Formation in Onion (Allium cepa L.)
Rashid, M.H.A., Cheng, W. & Thomas, B. Sci Rep 9, 14629 (2019). https://doi.org/10.1038/s41598-019-51262-1.

Removal of Pb(II) by Pellicle-Like Biofilm-Producing Methylobacterium hispanicum EM2 Strain from Aqueous Media
Jeong, Sun-Wook, Kim, Hyo Kyeong, Yang, Jung Eun, Choi, Yong Jun. Water 2019, 11(10), 2081; https://doi.org/10.3390/w11102081.

Molecular characterization of common bean curly stunt virus: a novel recombinant geminivirus in China
Zhang, R., Wu, X., Jiang, X. et al. Arch Virol 165, 257–260 (2020). https://doi.org/10.1007/s00705-019-04473-w.

Occurrence and distribution of begomoviruses infecting tomatoes, peppers and cucurbits in Thailand
Charoenvilaisiri, S., Seepiban, C., Phironrit, N, et al. Crop Protection, Volume 127, 2020, 104948, ISSN 0261-2194, https://doi.org/10.1016/j.cropro.2019.104948.

Population Genetics Revealed a New Locus That Underwent Positive Selection in Barley
Reinert, Stephan, Osthoff, Alina, Léon, Jens, Nas, Ali Ahmad. Int. J. Mol. Sci. 2019, 20(1), 202; https://doi.org/10.3390/ijms20010202.

Sodium Butyrate Modulates Mucosal Inflammation Injury Mediated by GPR41/43 in the Cecum of Goats Fed a High Concentration Diet
Chang G, Ma N, Zhang H, Wang Y, Huang J, Liu J, Dai H and Shen X. Front. Physiol. 2019, 10:1130. doi: 10.3389/fphys.2019.01130.

Variation and inheritance of the XanthomonasraxX‐raxSTAB gene cluster required for activation of XA21‐mediated immunity
Liu, F., McDonald, M., Schwessinger, B., Joe, A., Pruitt, R., Erickson, T., Zhao, X., Stewart, V. and Ronald, P.C. (2019). Molecular Plant Pathology, 20: 656-672. doi:10.1111/mpp.12783.

Purification and Characterization of Pathogenesis Related Class 10 Panallergens
McBride, J. Cheng, H., Maleki, S, Hurlburt, B. Foods 2019, 8(12), 609; https://doi.org/10.3390/foods8120609.

Complete Genome Sequence of the Plantaricin-Sensitive Strain Lactobacillus plantarum NCIMB 700965
Heeney DD, Marco ML. 2019. Microbiol Resour Announc 8:e01724-18. https://doi.org/10.1128/MRA.01724-18.

Systematic evasion of the restriction-modification barrier in bacteria
Johnston, C., Cotton, S., Rittling, S., Starr, J., Borisy, G., Dewhirst, F., Lemon, K. Proceedings of the National Academy of Sciences Jun 2019, 116 (23) 11454-11459; DOI: 10.1073/pnas.1820256116.

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Every bit the match of Vector NTI
“I’ve found the package to be excellent and exemplary. In particular, the SeqBuilder module is very versatile and every bit the match of Vector NTI.”
Dr. Chris Winefield, Lincoln University
Highly recommend
“I really like SeqBuilder…it makes looking at my sequences like child’s play. I would highly recommend it to any genetics or molecular biology lab.”
Takaaki Watanabe, National Institute for Basic Biology
Intuitive interface
“Easy to use, intuitive interface, makes working with sequences easy.”
Matthew Nilles, University of North Dakota

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