Serial cloner feature import genbank software#
Serial cloner feature import genbank mac#
Serial cloner feature import genbank windows#

Serial cloner feature import genbank software#

The NCBI sequence databases and software tools are designed around a particular model of biological sequence data. The Data Model section outlines the NCBI model for biotechnology information, which is centered on the concept of a biological sequence as a simple, linear coordinate system.Īssociating Annotations With Locations On Biological SequencesĬollections of Related Biological Sequences The following is an outline of the topics presented in this chapter: Francis OuelletteĬhapter 2 - The NCBI Data Model Chapter Outline Another good source of information about the NCBI data model is:Ī Practical Guide to the Analysis of Genes and ProteinsĮdited by Andreas D. ASN.1 type names and the corresponding C++ class or data member names are used almost interchangeably throughout the chapter. This chapter describes the NCBI Biological Sequence Data Model, with emphasis on the ASN.1 files and C++ API. If you think that ApE doesn't find all of the ClaI sites (or XbaI or BclI) that you KNOW are present in your sequence, turn off the Dam/Dcm methylation on your sequence and try again.Biological Sequence Data Model Introduction In ApE, open the FASTA file, then use the Features menu to open the GFF3 track info.Īnother way to go is to take the gene model (from a gene page), paste it into an ApE window and then select all, make a new feature (Feature menu), and in the edit feature window that appears press the 'upper case only' button. You can add the feature tracks by downloading the GFF3 feature track files using the same menu. gff file in the latest ApE.Īlternatively, you can export a genomic region (from the genome viewer) as a FASTA formatted file (using the menu on the upper left). UNCHECK 'Include track configuration data'. Dump selected features using version 3 Across currently visible region. You can now export genomic regions from Wormbase directly: In the upper right drop-down menu button, select 'Download Track Data'. Finds translationally silent restriction sitesĬlick here to make a voluntary donation in support of ApE.Aligns two DNA sequences (or any combination of sequence and ABI trace), with the alignment hyperlinked to the original sequence.Finds potential primers matching user criteria (length, Tm, %GC, self/other complementarity).Translates sequences with optional DNA alignment.Graphic maps that show primer binding sites and all interesting sequence features.Sequence to be annotated and visualized in multiple ways quickly and efficiently.Quick searching and highlighting of all available primers that you (or others) have that hybridize to a sequence.Uses custom feature definition libraries, which allow:.

Serial cloner feature import genbank windows#

Most analysis windows are hyperlinked to their corresponding sequences, including:.Imports DNA Strider format files (simple enzyme, site lists) available from REBASE.Allows users to define new enzymes by name and recognition site.Has user defined enzyme grouping to distiguish eg.Selects sites that cut more often in one sequence than another (for snip-SNP detection or diagnostic digests).Selects sites matching multiple criteria (union/intersection- cut frequency, site type) in all open windows.Sequences in ABI traces can be aligned directly to a reference sequence, with the alignment hyperlinked back to te trace.Draws pre-defined and user-defined DNA ladders.Copy and save graphics as Windows metafiles (MS Windows only).Saves graphics as encapsulated postscript or scalable vector graphics.

Connects graphic and text features with hyperlink double click.

Creates graphic restriction maps- linear or circular with features indicated.

Text map shows DNA sequence, translation, and features as text-based graphics.

Directly BLASTs selected sequence at NCBI or wormbase.

Highlights and draws graphic maps using feature annotations from genbank and embl files.

Saves files as DNA Strider-compatible or Genbank file format.

Reads DNA Strider, Fasta, Genbank and EMBL files.

Shows translation, Tm, %GC, ORF of selected DNA in real-time.

Highlights text using pre-defined and custom feature libraries.

Accurately reflects Dam/Dcm blocking of enzyme sites.

Highlights restriction sites in the editing window.

Serial cloner feature import genbank mac#

Runs in Windows (XP, Vista, 7, 8, and 10) and Mac (OS X v10.11 and above).