Molecular Biology

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

Vineet Gopal avatar Somak Das avatar Saif Hakim avatar +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
Anshi Saxena avatar
Written by Anshi Saxena
Updated over a week ago

Edit DNA sequences

Insert or delete base pairs in a DNA sequence.
Alex Chao avatar
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.
Damian Costello avatar
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.
Somak Das avatar
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
Lauren Shields avatar
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
Stefan Siegfried avatar
Written by Stefan Siegfried
Updated over a week ago

Codon optimize DNA sequences

Use Benchling's nucleotide codon optimization tool for improved protein expression.
Ashoka Rajendra avatar
Written by Ashoka Rajendra
Updated over a week ago

Use parts to design modular sequences

Nest one sequence within another sequence.
Saif Hakim avatar
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.
Aishwarya Pattnaik avatar
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.
Andrew Collins avatar
Written by Andrew Collins
Updated over a week ago

Share a sequence file

Easily generate a link to share individual sequence files.
Aishwarya Pattnaik avatar
Written by Aishwarya Pattnaik
Updated over a week ago

Lock a sequence file

Lock sequence files to prevent accidental edits.
Nishant Neel avatar
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
Michael Wu avatar
Written by Michael Wu
Updated over a week ago
Primers

Import primers

Quickly import existing primer databases.
Aishwarya Pattnaik avatar
Written by Aishwarya Pattnaik
Updated over a week ago

How is primer melting temperature (Tm) calculated?

Freeman Cherng avatar
Written by Freeman Cherng
Updated over a week ago

Export primers

Export all primers or oligos attached to a sequence or within a folder.
Nishant Neel avatar
Written by Nishant Neel
Updated over a week ago

How can I view all of my primers?

Damian Costello avatar
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.
Johnny Truong avatar
Written by Johnny Truong
Updated over a week ago

How can I archive primers?

Damian Costello avatar
Written by Damian Costello
Updated over a week ago

How can I detach primers from a sequence?

Damian Costello avatar
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.
Aishwarya Pattnaik avatar
Written by Aishwarya Pattnaik
Updated over a week ago

Attach saved primers

Find and attach saved primers to sequences.
Nishant Neel avatar
Written by Nishant Neel
Updated over a week ago

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

Damian Costello avatar
Written by Damian Costello
Updated over a week ago

How can I link primers and create primer pairs?

Johnny Truong avatar
Written by Johnny Truong
Updated over a week ago

Attach primers to multiple sequences

Select multiple sequences and attach primers in bulk.
Ashoka Rajendra avatar
Written by Ashoka Rajendra
Updated over a week ago

Run PCR in silico

Model a PCR reaction and see your PCR product in Benchling.
Damian Costello avatar
Written by Damian Costello
Updated over a week ago

Primers FAQ

Get answers to frequently asked questions about viewing, using, and designing primers.
Lily Helfrich avatar
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
M
Written by Meghan Bosch
Updated over a week ago

Can I realign traces after trimming them?

Vedika Sridhar avatar
Written by Vedika Sridhar
Updated over a week ago

How do I specify a template sequence?

Damian Costello avatar
Written by Damian Costello
Updated over a week ago

Upload trace (.ab1) files

Upload and view .ab1 files on Benchling
Lauren Shields avatar
Written by Lauren Shields
Updated over a week ago

How do I align multiple sequences at once?

Damian Costello avatar
Written by Damian Costello
Updated over a week ago

Viewing and managing alignments

Sakura Schweizer avatar
Written by Sakura Schweizer
Updated this week

Alignments FAQ

Get answers to frequently asked questions about performing and modifying alignments in Benchling.
Lily Helfrich avatar
Written by Lily Helfrich
Updated over a week ago

How can I add new sequences to an existing alignment?

Aishwarya Pattnaik avatar
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
Sakura Schweizer avatar
Written by Sakura Schweizer
Updated this week

Can I rearrange the order of sequences in an alignment?

Damian Costello avatar
Written by Damian Costello
Updated over a week ago

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

Lauren Shields avatar
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.
Ashoka Rajendra avatar
Written by Ashoka Rajendra
Updated over a week ago

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

Lauren Shields avatar
Written by Lauren Shields
Updated over a week ago

How can I scroll horizontally through an alignment?

Lauren Shields avatar
Written by Lauren Shields
Updated over a week ago

How do I export my DNA alignment?

Export DNA alignments to PDF, FASTA, or Clustal
Ashoka Rajendra avatar
Written by Ashoka Rajendra
Updated over a week ago