Molecular Biology

Annotate sequences, design primers, perform alignments, and model assemblies using rich design and analysis tools

+22

95 articles in this collection
Written by Vineet Gopal, Somak Das, Saif Hakim and 22 others

Sequences

Importing DNA sequences

Import DNA sequences from public databases or from your computer

Written by Anshi Saxena
Updated over a week ago

Edit DNA sequences

Insert or delete base pairs in a DNA sequence.

Written by Alex Chao
Updated over a week ago

View DNA sequences and change display features

Manage the display of a DNA sequence and its features.

Written by Damian Costello
Updated over a week ago

Search sequences for features

Navigate to features such as annotations and ORFs, and search sequences for specific bases or regions.

Written by Somak Das
Updated over a week ago

Update the index on a DNA sequence

Update the start index of or re-index a DNA sequence

Written by Lauren Shields
Updated over a week ago

Send your sequence to NCBI BLAST

Have your sequence or section of your sequence sent out to NCBI BLAST

Written by Stefan Siegfried
Updated over a week ago

Codon optimize DNA sequences

Use Benchling's nucleotide codon optimization tool for improved protein expression.

Written by Ashoka Rajendra
Updated over a week ago

Use parts to design modular sequences

Nest one sequence within another sequence.

Written by Saif Hakim
Updated over a week ago

Access and restore an old version of a sequence

Learn how to view a sequence's version history and revert to old versions.

Written by Aishwarya Pattnaik
Updated over a week ago

Auto-Fill Translations

Have Benchling automatically detect and fill in valid translation links to associate AA entities to the DNA entities that encode them.

Written by Andrew Collins
Updated over a week ago

Share a sequence file

Easily generate a link to share individual sequence files.

Written by Aishwarya Pattnaik
Updated over a week ago

Lock a sequence file

Lock sequence files to prevent accidental edits.

Written by Nishant Neel
Updated over a week ago

Export DNA Sequences (.gb, .fasta, .csv, .svg, .rdf, .zip)

Easily export sequence files individually or in bulk

Written by Michael Wu
Updated over a week ago

Annotations

Annotate antibody specific information on protein sequences

Characterize antibody chain variable domains.

Written by Andrew Collins
Updated over a week ago

Create and edit sequence annotations

Annotate important regions on DNA or amino acid sequences.

Written by Hoang Ha
Updated over a week ago

Auto-annotate sequences

Auto-annotate your DNA or amino acid sequences automatically using your feature libraries.

Written by Hoang Ha
Updated over a week ago

Create a feature library for auto-annotation

Create an annotation, or DNA feature library.

Written by Vineet Gopal
Updated over a week ago

Annotations FAQ

Get answers to frequently asked questions about annotating sequences in Benchling.

Written by Lily Helfrich
Updated over a week ago

Primers

Import primers

Quickly import existing primer databases.

Written by Aishwarya Pattnaik
Updated over a week ago

How is primer melting temperature (Tm) calculated?

Written by Freeman Cherng
Updated over a week ago

Export primers

Export all primers or oligos attached to a sequence or within a folder.

Written by Nishant Neel
Updated over a week ago

How can I view all of my primers?

Written by Damian Costello
Updated over a week ago

Design primers manually

Design single or paired primers and verify your primers by checking secondary structures, melting temperature (Tm), and GC content.

Written by Johnny Truong
Updated over a week ago

How can I archive primers?

Written by Damian Costello
Updated over a week ago

How can I detach primers from a sequence?

Written by Damian Costello
Updated over a week ago

Design primers with the primer wizard

Design primers directly on a sequence using the Primer Wizard.

Written by Aishwarya Pattnaik
Updated over a week ago

Attach saved primers

Find and attach saved primers to sequences.

Written by Nishant Neel
Updated over a week ago

How can I toggle the visibility of bases for attached primers?

Written by Damian Costello
Updated over a week ago

How can I link primers and create primer pairs?

Written by Johnny Truong
Updated over a week ago

Attach primers to multiple sequences

Select multiple sequences and attach primers in bulk.

Written by Ashoka Rajendra
Updated over a week ago

Run PCR in silico

Model a PCR reaction and see your PCR product in Benchling.

Written by Damian Costello
Updated over a week ago

Primers FAQ

Get answers to frequently asked questions about viewing, using, and designing primers.

Written by Lily Helfrich
Updated over a week ago

Alignments

Generating reverse complements for .ab1 files

Reverse complement .ab1 files while maintaining the trace file

Written by Meghan Bosch
Updated over a week ago

Can I realign traces after trimming them?

Written by Vedika Sridhar
Updated over a week ago

How do I specify a template sequence?

Written by Damian Costello
Updated over a week ago

Upload trace (.ab1) files

Upload and view .ab1 files on Benchling

Written by Lauren Shields
Updated over a week ago

How do I align multiple sequences at once?

Written by Damian Costello
Updated over a week ago

Viewing and managing alignments

Written by Sakura Schweizer
Updated this week

Alignments FAQ

Get answers to frequently asked questions about performing and modifying alignments in Benchling.

Written by Lily Helfrich
Updated over a week ago

How can I add new sequences to an existing alignment?

Written by Aishwarya Pattnaik
Updated over a week ago

Creating consensus and template alignments

Align one or many DNA sequences or trace files to a template sequence

Written by Sakura Schweizer
Updated this week

Can I rearrange the order of sequences in an alignment?

Written by Damian Costello
Updated over a week ago

Why can't I see my traces on my alignments?

Written by Lauren Shields
Updated over a week ago

How do I view reading frames on DNA alignments?

Look at all possible amino acid sequences for a given DNA sequence in an alignment.

Written by Ashoka Rajendra
Updated over a week ago

How do I trim the traces that I'm aligning?

Written by Lauren Shields
Updated over a week ago

How can I scroll horizontally through an alignment?

Written by Lauren Shields
Updated over a week ago

How do I export my DNA alignment?

Export DNA alignments to PDF, FASTA, or Clustal

Written by Ashoka Rajendra
Updated over a week ago

Restriction Enzymes and Digests

How can I specify which restriction enzyme cut sites are visible on my sequence?

Written by Lauren Shields
Updated over a week ago

Create lists of restriction enzymes

Create your own enzyme lists that represent the enzymes in your organization's inventory, and share them.

Written by Nishant Neel
Updated over a week ago

Find restriction enzyme cut sites

Search for restriction enzymes and visualize them on your sequence maps.

Written by Nishant Neel
Updated over a week ago

How can I search for restriction enzymes by single, double, or no cutters?

Written by Damian Costello
Updated over a week ago

Simulate a digest

Perform a virtual restriction enzyme digest in Benchling and model your expected results.

Written by Nishant Neel
Updated over a week ago

How can I see restriction enzymes that don't cut in my selection but do cut outside of my selection?

Written by Damian Costello
Updated over a week ago

Restriction Enzymes and Digests FAQ

Get answers to frequently asked questions about visualizing restriction enzyme cut sites and performing virtual digests in Benchling.

Written by Lily Helfrich
Updated over a week ago

When I click high-fidelity enzymes, why are other restriction enzymes marked unavailable?

Written by Lauren Shields
Updated over a week ago

How do I create custom ladders to use in virtual digests?

Written by Damian Costello
Updated over a week ago

Cloning and Assembly Wizards

Clone by copy and paste

Digest and ligate an assembly by a simple copy and paste method.

Written by Nishant Neel
Updated over a week ago

How do I open the Assembly Wizard?

Written by Aishwarya Pattnaik
Updated over a week ago

Clone using the Digest and Ligate Assembly Wizard

Perform a digest and ligate assembly using the Benchling Assembly Wizard.

Written by Lauren Shields
Updated over a week ago

Can I perform a Gibson assembly with fragments that are already digested?

Written by Lauren Shields
Updated over a week ago

Clone using the Gibson Assembly Wizard

Perform a Gibson assembly using the Benchling Assembly Wizard.

Written by Lauren Shields
Updated over a week ago

What is the ideal annealing temperature and primer melting temperature (Tm) for Gibson assembly?

Written by Lauren Shields
Updated over a week ago

Clone using the Golden Gate Assembly Wizard

Perform a Golden Gate assembly using the Benchling Assembly Wizard.

Written by Lauren Shields
Updated over a week ago

How does the Gibson Assembly Wizard factor in 5' and 3' overhangs?

Written by Damian Costello
Updated over a week ago

Assembly Wizard FAQ

Get answers to frequently asked questions about the Benchling Assembly Wizard.

Written by Lily Helfrich
Updated over a week ago

Can I maintain restriction sites when using the Gibson Assembly Wizard?

Written by Lauren Shields
Updated over a week ago

Bulk Assembly

Learn the basics of Bulk DNA Assembly

Navigate to and familiarize yourself with Benchling's Bulk Assembly tool.

Written by Damian Costello
Updated over a week ago

Navigate to the Bulk Assembly Wizard

assemble combinatorial plasmids maps in bulk by navigating to the bulk assembly wizard

Written by Brandon Kirk
Updated over a week ago

Protein Analysis

Import proteins

Learn to import import directly from your computer or from databases like NCBI or UniProt.

Written by Damian Costello
Updated over a week ago

Analyze protein properties

Get important information about your protein such as molecular weight, isoelectric point, and extinction coefficient.

Written by Damian Costello
Updated over a week ago

How are protein characteristics calculated?

Description of how Benchling calculates various protein properties.

Written by Vedika Sridhar
Updated over a week ago

Create, view and analyze translations

Translate a DNA sequence, create an annotation and generate biochemical properties for that translation.

Written by Madeleine Flick
Updated over a week ago

Back translate an AA sequence

Use Benchling's nucleotide codon optimization tool to back translate an AA sequence to a DNA sequence.

Written by Ashoka Rajendra
Updated over a week ago

Export a protein

Export an amino acid sequence in FASTA or GenPept format

Written by Tara Lee
Updated over a week ago

Perform consensus or template alignments on protein sequences

Use our protein alignment tool to view consensus proteins, or compare proteins against a template.

Written by Damian Costello
Updated over a week ago

Protein Structure Prediction (Beta)

Join the protein structure prediction (beta) waitlist

Request access to our beta feature for protein structure prediction using AlphaFold.

Written by Lily Helfrich
Updated over a week ago

Predict protein structures (beta)

Test our beta feature for protein structure prediction using AlphaFold.

Written by Lily Helfrich
Updated over a week ago

Modified Oligos

Modified Oligonucleotides: Adding/Removing Modified Oligonucleotides in a Sequence

Learn how to edit Modified Oligo sequences

Written by Andrew Mecca
Updated over a week ago

Modified Oligonucleotides: The Monomer Library

Learn about Benchling’s Monomer Library

Written by Andrew Mecca
Updated over a week ago

Modified Oligonucleotides: HELM/IDT Notation

Learn about Benchling's HELM/IDT notation

Written by Andrew Mecca
Updated over a week ago

Modified Oligonucleotides: Search & Filter

Learn how to search and filter for Modified Oligos on Benchling

Written by Andrew Mecca
Updated over a week ago

Modified Oligonucleotides: Sequence Navigation & Visualization

Learn how to visualize Modified Oligos on Benchling

Written by Andrew Mecca
Updated over a week ago

Working with Modified Oligonucleotides in Benchling

Learn how to use Modified Oligos on Benchling

Written by Andrew Mecca
Updated over a week ago

Introduction to Modified Oligonucleotides

Learn the foundations of Modified Oligos on Benchling

Written by Andrew Mecca
Updated over a week ago

CRISPR

Why am I getting the error "Distinct type IIS enzyme cut sites were not found at the specified start and end"?

Written by Thomas Wu
Updated over a week ago

How are on-target scores calculated?

Written by Aishwarya Pattnaik
Updated over a week ago

Design guide RNAs (gRNAs)

Design and analyze gRNAs for CRISPR.

Written by Lauren Shields
Updated over a week ago

How are off-target scores calculated?

Written by Nishant Neel
Updated over a week ago

Why are my paired nickase scores lower than my single guide scores?

Written by Nishant Neel
Updated over a week ago

Assemble guide RNAs (gRNAs) into plasmids

Assemble your CRISPR gRNA into a plasmid.

Written by Lauren Shields
Updated over a week ago

Why can I only see a finite number of off-target sites?

Written by Lauren Shields
Updated over a week ago

Design homologous recombination (HR) templates

Design homologous recombination (HR) ssODN templates for CRISPR-directed HR.

Written by Lauren Shields
Updated over a week ago

CRISPR FAQ

Get answers to frequently asked questions about our CRISPR tools, including questions about algorithms and scores.

Written by Nishant Neel
Updated over a week ago

How do I set the genomic region of my imported sequence?

Written by Lauren Shields
Updated over a week ago

Export a table of on-target or off-target scores and sites from your CRISPR experiment

Written by Lauren Shields
Updated over a week ago