BxSeqTools - An Innovative Molecular Biology Sequence Analysis and Data Management System

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BxSeqTools > Help > Quick Start Guide

BxSeqTools Descriptions

	Quick Start Guide of BxSeqTools
	Get molecule sequences into the system
	Open Sequences Search Sequences Browse Sequences Import Sequences
	Perform basic sequence manipulations
	Edit Sequences Sequence Manaipulation Save Sequences into Database
	Restriction site analysis
	Select Favorate Enzymes List Restriction Enzyme Sites Restriction Enzyme Site Maps
	Sequence alignment
	Align Two DNA Sequences Align Multiple Sequences (DNA or Protein) Format Alignment Results
	Design, browse, and search oligos and primers
	Design Sequencing Primers Find Matched Primers Browse Saved Oligos and Primers Import Oligos and Primers Save New Oligos into Database Save Auto-Designed Oligos into Database
	Molecular cloning Ultimate Molecular Cloning Guides
	Basic Cloning Sub-Cloning: Uses restriction endonucleases to digest both vector and insert DNA and uses ligases to ligate fragments. PCR Cloning: Uses PCR reaction to amplify DNA fragment, followed by sub-cloning. Gene Synthesis: Uses DNA oligos to synthesis gene without source DNA, followed by sub-cloning. TOPO Cloning TA TOPO Cloning: Cloning without using restriction endonucleases, but insert orientation is unknown. Directional TOPO Cloning: Cloning without using restriction endonucleases, insert has one orientation Gateway Cloning: A cloning method based upon the site specific recombination of lambda bacteriophage.

	BxSeqTools Descriptions for All Users
	Get molecule sequences into the system
	Open Sequences - This tool allows to load sequence from GenBank, a local file, databases that were saved previously, or copy-paste directly. Three formats are supported: text, fasta, or genbank format. Search Sequences - This tool allows searching and retrieving sequences from GenBank without leaving BxSeqTools. You can retrieve cDNA, genomic DNA, or protein sequences with one search. Due to integration and automation, this tool can greatly speed up your research. Browse Sequences - This tool allows browsing the database for all stored sequences. Import Sequences - This tool allows importing multiple sequences from a compressed file. Save your data in database: the opened sequences are stored in "memory" temporarily. If you close your browser or logout the system, the opened sequences will be lost permanently. Therefore, make sure you save your sequences in database before closing your browser.
	Perform basic sequence manipulations
	Edit Sequences - This tool allows annotating sequence information in GenBank format. It can also be used to convert other format to GenBank format. You can save changes temporarily or save sequences permanently in databases. Additional functions include viewing sequence with restriction sites and open reading frames, updating GenBank file headers, adding features automatically, adding features manually, deleting features, deleting feature qualifiers, and more. Sequence Manaipulation - This provides various tools to manipulate sequences, such as translation, reversing sequences, generating reverse-complementary sequences, formating sequences, and more. Save Sequences into Database - BxSeqTools allows saving your cloning methods, annotated or designed constructs, and designed primers online directly.
	Restriction site analysis
	Select Default Analysis Enzymes - This tool sets up the default restriction enzymes that will be used in many sequence analysis tools. List Restriction Enzyme Sites - This tool lists available restriction enzyme sites on any sequences. Restriction Enzyme Site Maps - This tool shows linear or circular Restriction Enzyme Sites Maps.
	Sequence Alignment
	Align Two DNA Sequences Smart Alignment: Uses "Smart" algorithms to perform sequence alignment: it tells you where the mismatchs are and highlight them for you. This method is best for comparing sequencing results with target sequences. This tool has been used broadly in SNP detection. Local Alignment: uses FASTA LALIGN program to align two sequences. The alignment results include multiple alignments of fragments from two sequences. Global Alignment: uses FASTA GGSEARCH program to align two sequences. The alignment is based on the overall sequences. Align Multiple Sequences (for both DNA or Protein). This tools uses ClustalW method to align multiple sequences. Users can also format the alignment results for publication purpose. Format Multiple Sequence Alignment Results. This tool allows formatting aligned multiple protein or DNA sequences in colors for publication purpose.
	Design, browse, and search oligos and primers
	Design Sequencing Primers - BxSeqTools provides one-click method to design optimized sequencing primers. The designed primers are optimized for Tm, GC%, secondary structure, and potential false priming! Find Matched Primers - BxSeqTools allows you to search all available primers for any sequences. You will be surprised how many primers can match your sequences! Browse Saved Oligos and Primers - This is the tool to browse and update stored oligos and primers. Import Oligos and Primers - This tool allows importing multiple oligos and primers into the databases. Save New Oligos into Database - You can save your own oligos/primers into the databases. The system will calculate the Tm, GC%, and others automatically. Save Auto-Designed Oligos into Database - BxSeqTools allows saving your cloning methods, annotated or designed constructs, and designed primers online directly.
	Molecular cloning
	Our Cloning Guide provides the simplest and most reliable way to perform virtual cloning. It supports all major cloning methods: Sub-cloning, PCR cloning, TA cloning, Directional TOPO cloning, and gene synthesis. It provides "foolproof" cloning: e.g. you can not make mistakes by choosing wrong restriction sites! It not only automatically generates GenBank-formatted, fully annotated construct, but also designs PCR primers for PCR Cloning method and Gene synthesis primers for Gene synthesis method.
	Basic Cloning Sub-Cloning: Uses restriction endonucleases to digest both vector and insert DNA and uses ligases to ligate fragments. PCR Cloning: Uses PCR reaction to amplify DNA fragment, followed by sub-cloning. Gene Synthesis: Uses DNA oligos to synthesis gene without source DNA, followed by sub-cloning. TOPO Cloning TA TOPO Cloning: Cloning without using restriction endonucleases, but insert orientation is unknown. Directional TOPO Cloning: Cloning without using restriction endonucleases, insert has one orientation Gateway Cloning: A cloning method based upon the site specific recombination of lambda bacteriophage.
	Other analyses
	DNA format conversion GC% analysis DNA restriction site analysis Open reading frame prediction Codon analysis Codon optimization Construct annotation Translation DNA sequence manipulation Protein sequence manipulation Protein reverse translation ...
	Manage your research data
	BxSeqTools provides integrated tools to manage Constructs and Oligos. BxSeqTools provides built-in multi-level security to customers data, BxSeqTools users share data with group members naturally. BxSeqTools users can publish constructs to the shared sequence database that can be accessed by all users.