Ape Plasmid Editor Manual

How to use this page

ApE (a plasmid editor) - Word (Microsoft Office). Sequence Editing The important things to remember when choosing a program: - Does it let me jump around the sequence based on coordinates? - How easy is it to combine two existing files? Sequence Editing. See posts, photos and more on Facebook. Well, you’ll go “ApE” over A Plasmid Editor, a program as simple in use as it is in name. ApE is free to download and runs across all three major platforms: Windows, OS X, and Linux/Unix.

Please help us by adding new digital resources useful to the community here. Keep this page organized by following the
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All of the links below are organized first by whether they are general reference or a more specified research tool.
The sub-categories are organized alphabetically by research topic. Note that many of the tools listed may fit into
multiple categories, but are only listed once. Tools of this type may be tagged with other relevant categories by
adding a link to another section of the page after the description. Use the _*link format of the following DNA example:

QIIME (Quantitative Insights Into Microbial Ecology) ^software Powerful suite of open source bioinformatics tools for performing microbiome analysis from raw sequences. _*RNA

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for downloadable items, and ^app for items used on phones and tablets. Please tag any additional categories in this
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Information resources

References, texts, and information resources.

Databases

Search engines and data repositories. There are thousands available (see MetaBase). The few items listed here are some of the broadest and most powerful

General Search/Reference

BioNumbers
- The database of useful biological numbers. (link to database)

CDC Disease Conditions
- Filtered index of diseases from the CDC database

EMBL-EBI
- Hugely extensive collection of resources, databases, and tools related to diverse aspects of bioinformatics and molecular biology, often containing everything one might need

Entrez (NCBI)
- Search all NCBI databases

MetaBase
- The database of biological databases - External link

Tree of Life
- Collaborative encyclopedia of biodiversity

Wolfram Alpha
- Computational server for finding/calculating summary data about a wide range of topics, plus useful widgets like reagent tables and gene lookup

Genome and Metabolism

BioCyc
- Collection of thousands of pathway/genome databases for many organisms, plus software tools for understanding their data

Colibri by Institut Pasteur
- E. coli genome browser; get sequences, see the position of your gene in the chromosome, see the function of your gene, and other fun stuff. You can also search for protein sequences/motifs within the E. coli genome.

EcoGene
- Database of all E. coli genes and sequences (Entrez data is pulled from here)

EcoCyc
- Comprehensive biochemical pathway and gene function site for E. coli

ENCODE
- Parts list for functional elements in the human genome

Ensembl
- Eukaryotic genome browser

Ensembl Genome
- Sister to Ensembl, not limited to Eukaryotes

Inventory of Composable Elements (ICE) - The public instance of the JBEI Registry
- A DNA part, plasmid, microbial strain, and Arabidopsis Seed online repository with physical sample tracking capabilities
- A site where you can explore the various features of the JBEI Registry software, and even get some work done!
- Try out the integrated online tools, including DNA sequence editing and annotation (Vector Editor) and auto-aligning sequencing trace files against a template.
- Follow a link to the underlying open-source software source code.

KEGG
- Genomic database geared towards high-level functions of the biological system

Mammalian Gene Collection
- Access to sequence-validated, full-length, protein-coding, mammalian cDNA clones

MetaCyc
- Multi-organismal member of BioCyc collection; catalogs entire universe of metabolism

SGD
- Saccharomyces genome database (yeast genome)

UCSC Genome Bioinformatics
- Sequence reference for a large number of genomes

Protein

Antibody Resource
- Enter a protein to search for antibodies and ELISA kits

BRENDA
- Comprehensive enzyme information system

ConSurf
- Server for the identification of functional regions in proteins

Genome3D
- Consensus structural annotations and 3D models for sequences of model organisms (built upon numerous other useful related resources)

Technical suppport on protein crystallization by Hampton Research
- Focused on protein crystallization but contains a lot of generally useful information about various reagents with respect to proteins.

UniProt
- Extensive database of protein sequence and functional information

RNA

Appendix by Ambion, Inc.
- Website with many useful nucleic acid parameters.

GreenGenes
- 16S rRNA database and workbench (most recently updated data can be downloaded here)

Ribosomal Database Project
- Quality-controlled, aligned and annotated Bacterial and Archaeal 16S rRNA sequences, and Fungal 28S rRNA sequences, and a suite of analysis tools

SILVA
- Massive, searchable rRNA database (especially strong for microbes)

Vectors

Addgene's Vector DB
- Addgene is a a non-profit plasmid repository where scientists can archive and share their plasmids. Addgene assists with data submission and all tech transfer issues. Plasmids can be requested from Addgene for a fee to cover expenses.
- AddGene Vectors can be directly imported into Genome Compiler software platform, in which you can easily edit and visualize it.

Lab Techniques

Barrick Lab of UT Austin
- Tons of helpful resources like protocols, guides, links, and tools for lab work

BenchFly
- Search, view, upload, create, and host scientific protocol videos

Current Protocols in Molecular Biology
- Handbook of protocols. (Links to Wiley Online Library)

Gene expression in E. coli by Ehrmann lab
- Tips and information on gene expression in E. coli

Molecular Cloning by Sambrook and Russell
- Handbook of protocols. Subscription only. External link

OWW Materials
- Useful information for making or obtaining reagents, enzymes, buffers, etc.

On Being a Scientist by National Academy of Science
- NAS report on responsible conduct in research.

OWW Protocols
- Growing collection of laboratory protocols and techniques

Polony Protocols by Church and Mitra Lab
- Polonies are colonies of PCR amplicons derived from a single molecule of nucleic acid.

Protocol-online by Dr. Long-Cheng Li
- A database of research protocols in a variety of life science fields. It has a popular discussion forum.

Protocols.io^app^web
- Huge, open access life science protocol repository for discovery and sharing of scientific methods

VADLO Search Engine
- VADLO is a search engine for Life Sciences Protocols, Online Tools, Databases, Software, and Biomedical Powerpoint Lectures. It also has Daily research cartoons, called *'Life in Research' Cartoons.

Microbial physiology

CyberCell Database (CCDB) by Institute for Biomolecular Design
- Several tables describing statistical data on E. coli compiled from several sources.

EcoSal by ASM Press
- An incomplete web version of the publication Escherichia coli and Salmonella: Cellular and Molecular Biology. (Subscription required)

Metabolic Pathways Poster PDF by SigmaAldrich
- Free digital version of the paper Metabolic Pathways map. Because it is a PDF, it is also searchable.

MicrobeWiki
- Student edited resource on microbes and microbiology (curated pages reviewed by microbiologists)

Teaching

Khan Academy (Biology)
- Selection of science videos and short courses, including the popular Crash Course series

PhET
- Interactive simulations for science and math

ScienceHack
- Search engine for science videos with a review system

Research Tools

Tools and applications to aid in research tasks.

General

Benchling^web
- Online apps for cloning, molecular biology, and analysis

Bioinformatics Toolbox from DNA2.0 ^web
- Contains many Javascript tools to do common tasks.

Cancer Genome Anatomy Project^web
- Resources and tools related to the characterization of cancer gene expression profiles

Experiment^web
- Crowdfunded scientific research

Genome Compiler^web^software
- A powerful, free online & downloadable genetic engineering all-in-one platform for molecular & synthetic biologists

FastPCR^software
- An integrated tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching

Galaxy^web
- Easy-to-use Bioinformatics manipulation tools for UCSC data

iGEM Parts Registry^web
- Formerly curated by MIT, this is an open repository of BioBricks; the place for all your standard biological parts.

Ingeneue by George von Dassow, Eli Meir, Edwin Munro, and Garret Odell at the Center for Cell Dynamics^software
- An open-source java program for modeling gene regulatory networks. Users can rapidly build networks by specifying their topology, initial conditions, connectivity, and known parameters. Ingeneue can then search/explore paramter space for desired behavior, simulate the effects of noise and mutation, and generate statistics/time graphs of the system.

MABL^web
- Reconstruct and analyze phylogenetic relationships between molecular sequences

OpenCFU^software
- Local cell colony counting software

MCDS^software
- All-in-one molecular cloning and genetic engineering design, simulation & management tool for complex synthetic biology and metabolic engineering project.

PaR-PaR Laboratory Automation Platform^web
- PaR-PaR allows researchers to use liquid-handling robots effectively, enabling experiments that would not have been considered previously. After minimal training, a biologist can independently write complicated protocols for a robot within an hour.

Pinecone by Serotiny ^web
- High-level design, analysis and transmission of protein constructs. Pinecone matches users' designs with CRO's or DNA synthesizers to produce genetic starting material (dsDNA, plasmid or purified protein). Facilitates mutation and combinatorial protein sets that benefit from manufacturing economies of scale.

PubChase^software^app
- Generates research article recommendations unique to each user. Site also has a special academic community.

Science Gateway^web
- Collection of science-related links, including links to journals, catalogs, and tools. See their about page.

Calculators

[GdmCl] and [Urea] from refractive index by Sosnick lab ^web
- GdmCl and urea concentration calculator from index of refraction.

OligoCalc Oligonucleotide Calculator ^web
- Calculate a number of parameters for your nucleotide polymers

Statistics to use from Saint John's University. ^web

DNA

Affymetrix Tools^software
- Microchip and SNP analysis software. DevNet Tools and other compatible programs also listed for download and use

Artemis by the Sanger Center ^software
- A free DNA sequence viewer and annotation tool (Java based). The Sanger Center also develops a number of other miscellaneous tools for download

BioEdit^software
- Windows-only sequence alignment editor (no longer maintained, but free to download)

BLAST^web
- Finds regions of similarity between biological sequences.

CLC Sequence Viewer^software
- Software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, graphical viewing, and output options.

Gene Design by Boeke lab ^web
- Collection of online tools for codon optimization and shuffling, restriction site editing, and so on.

GeneDesigner by DNA2.0 ^software
- Combine genetic building blocks by drag-and-drop, codon optimize, restriction site editing, sequence oligo design etc. See BMC Bioinformatics 2006 Jun 6;7(1):285 for more detail.
- Free to download and works on Mac or PC. User agreement is somewhat restrictive, i.e. you cannot sell genes designed using the tool without permission.

GeneWarrior^web
- Free/simple online toolset for sequence manipulation

Genome Compiler^web^software
- The Complete set of tools for sequence viewing, annotation and alignment. Free online & downloadable and supports all file formats

IDT SciTools^web
- A number of web tools and calculators to assist in the design and execution of molecular biology research

Jalview^software
- Program for multiple sequence alignment editing, visualization, and analysis

NEB Cutter by New England Biolabs, Inc. ^web
- Tool for finding restriction sites, et cetera.

PerlPrimer^software
- Open source PCR primer design. Written in Perl/Tk.

Primer3^web
- Tool that lets you pick & evaluate primers from a DNA sequence

QIIME (Quantitative Insights Into Microbial Ecology) ^software
- Powerful suite of open source bioinformatics tools for performing microbiome analysis from raw sequences.

Rare Codon Calculator (RaCC) by NIH MBI Laboratory for Structural Genomics and Proteomics ^web
- Finds rare codons in a coding sequence.

Search of rare codons in nucleotide sequence by 'Practical Molecular Biology' ^web

Sequence file format converter from NIH ^web
- Web tool for converting between sequence file formats.

Sequence Manipulation Suite^web
- Quickly access a host of tools for analyzing and manipulating DNA, RNA, and protein sequences

SIDD^web
- Stress induced DNA duplex destabilization. Finds destabilized sites in superhelical DNA.

UNAFold^web
- Replacement for mFold for predicting nucleic acid folding. Downloadable and some applications are available online also.

USEARCH^software
- High throughput sequence analysis (orders of magnitude faster than BLAST) and other software tools

RNA

RBS Calculator in Genome Compiler
- Control translation initiation rate and predict protein production levels.

Promoter prediction^web
- both prokaryote and eukaryotic promoter prediction

UNAfold by Michael Zuker. ^web
- Apps for predicting RNA and DNA folds, calculating Tm's and free energies. Runs mfold + UNAfold servers

Sfold^web
- Statistical Folding and Rational Design of Nucleic Acids. Predicts accessible RNA sites

Vienna RNA^software
- RNA secondary structure prediction and design

XRNA^software
- Java tools for creating RNA secondary structure diagrams

Protein

RBS Calculator in Genome Compiler
- Control translation initiation rate and predict protein production levels

AGADIR by Serrano lab ^web
- An algorithm to predict the helical content of peptides.

AVID by Keating lab ^web
- An integrative framework for discovering functional relationships among proteins.

Backbone-dependent rotamer library by Dunbrack lab ^web
- Libraries of sidechain rotamer from protein structures

Cn3D by NCBI ^web
- A helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. It doesn't read PDB files but can be more straightforward to use than DeepView.

Contact Order Calulator by Baker lab ^web
- Calculator to determine a protein's contact order

Dang by Richardsons' lab ^software
- A command-line tool that generates a table of several useful geometric measurements for each residue or base from a PDB file.

DeepView by GlaxoSmithKline & Swiss Institute of Bioinformatics ^software
- Awesome program for viewing and studying protein structure.

ExPASy Proteomics server by the Swiss Institute of Bioinformatics ^web
- Collection of links to many pages to calculate parameters of your favorite proteins
1. Compute pI/Mw
  - A tool which allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of Swiss-Prot and/or TrEMBL entries or for user entered sequences.
2. ProtParam
  - A tool which allows the computation of various physical and chemical parameters for a given protein stored in Swiss-Prot or TrEMBL or for a user entered sequence.
3. Translate
  - Translate is a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.

GETAREA by Sealy Center for Structural Biology ^web
- Solvent accessible surface areas, atomic solvation energies, and their gradients for macromolecules

Metazome^web
- Proteome-level phylogeny and genomics

Modeller by Sali lab ^software
- Program for homology or comparative modeling of protein three-dimensional structures by satisfaction of spatial restraints.

PAIRCOIL2 by Keating and Berger labs ^web
- Tool to predict the parallel coiled coil fold from sequence using pairwise residue probabilities.

Another Plasmid Editor

ProteinProspector by UCSF Mass Spectrometry Facility ^web
- Proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments.

PyMOL^software
- Molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. The latest version does not run on OSX 10.3. (from Kathleen).

VMD by Theoretical and Computational Biophysics Group at UIUC ^software
- Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Generates pretty high resolution pictures of protein structures.

Zinc Finger Tools by Barbas lab ^web
- Design Zinc Finger DNA binding proteins

Vectors

ApE A plasmid Editor ^software
- Simple tools for plasmid design and manipulation

GeneDesigner by DNA 2.0 ^software
- Design genes de novo with a powerful and intuitive user interface

Genome Compiler^web^software
- A free all-in-one platform for intuitive vector design and automatic assembly. Supports main construction techniques, manual and auto sequence annotation, alignment, primer design and compatible to all file formats.

j5, DeviceEditor, and VectorEditor^web
- j5: DNA assembly design automation for (combinatorial) flanking homology (e.g., SLIC/Gibson/CPEC/SLiCE/yeast) and type IIs-mediated (e.g., Golden Gate/FX cloning) assembly methods
- DeviceEditor: a visual DNA design canvas that serves as front-end for j5
- VectorEditor: a visual DNA editing and annotation tool

PlasMapper^web
- Generates and annotates a plasmid map based on sequence data

Serial Cloner^software
- Light and intuitive tools for diverse molecular biology manipulations

SnapGene Viewer^software
- Free version of SnapGene. Allows mapping of DNA up to 1 Gb in length. Convenient viewing and annotation tools for genetic constructs.

Vector NTI^software
- Powerful but expensive vector editor. Supports most sequence types and easily manipulates genetic constructs.

Writing/Composition/Organization

CambridgeSoft^software
- Numerous proprietary applications for research and composition (ChemBioDraw is usually accessible via academic institution email)

Coredemia^web
- Community for sharing and discussion of research papers

Google Documents by Google^web
- Sharable, web-based word processing, spreadsheets, and presentations