The software is able to read and write DNA Strider-readable files and automatically import and exports data into the universal FASTA file format. The software has a graphical user interface (GUI) that makes sequencing and visualizing data easy and fast. ![]() The manual will show you the basic workflow that is involved with sequencing, cloning, and analyzing DNA samples. To give you an idea about how Serial Cloner works, let us take a look at the program's manual and how to use it. The software is available for purchase on the web and for download straight from the company's website. This software can be used by anyone with a Windows computer. STING Millenium - web-based suite of programs for visualizing molecular structure and comprehensive structure analysis:ĬASTp - webserver for identification and measurements of surface accessible pockets as well as interior inaccessible cavitiesSerial Cloner is an awesome software tool that allows users of molecular biology research to quickly and easily sequence, analyze, visualize, analyze, and interpret the data obtained during their experiments. PARVATI anisotropic displacement parameters statisticsįADE and PADRE - Shape and Complementarity Server NCONT - (ccp4) analyses contacts between subsets of atoms in a PDB file VADAR (Volume, Area, Dihedral Angle Reporter) SURFACE and AREAIMOL (ccp4) -surface programsĬastP - Volume and surface calculation of pocket or cavity VOIDOO - look for interior cavities, volumes of particular cavities (like active sites) Monster - A tool for inferring non-covalant interactions in proteins Protein Interaction Server - to obtain surface calculations NACCESS - Surface area calculaitons, per residue, or atom LIGPLOT/LigPlus/DIMPLOT - Interactions around a ligand or interface SiteEngine - wesite to define a active site and then search the PDB for similar sites. PDBredo - a site where they re-refined everyone's structures ProtBud - PC program to evaluate multimer contacts and compare to related structures. PISA-Protein Interfaces, Surfaces and Assemblies (using PDB or new coordinates) SCOP - Structural Classification of Proteins MUSTANG - A MUtiple STructure AligNment alGorithm Indonesia - USF's biological sequence analysis (not installed) - multiple sequence alignments STRAP - Multiple Structural/Sequence Alignment POSA - Partial Order Structural Alignments MATRAS - MArkovian TRAnsition of Structure evolution - does multiple alignments STAMP - Structural Alignment of Multiple Proteins (several choices) SSM - Secondary Structure Matching - multiple PDB comparison and sequence alignments. ![]() MSDServer - Macromolecular Structure Database (Can provide %similarity cutoff to see entire structural family) ![]() VAST - (NCBI) Vector Alignment of Search Tool - protein structural neighbors IP6-activated fusion proteins: maps, paper, protocol, Vector sequence (2000) A modular Set of Prokaryotic and Eukaryotic Expression Vectors Analytical Biochemistry 277, 109-120): pKA8 complete DNA sequence, pKA8 Cloning Map, Original Cloning Paper description Yeast Vectors: pYES2.0, pTF162, Stuff from Tim's lab about this series of vectorsīaculoVirus Vectors: pAcGP67-A for expression with a signal sequence for secretion PGEX Vectors: pGEXvectors, pGST-parallel, pGST-PP and pGST-TEV vectors from Steve (additional GST-PP and TEV vector sequences) Modified pET Vectors: pET11a-His(7)-PP, pET16b-TEV PET151-TOPO Cloning site map and full vector mapĭUET Vectors: pACYDuet-1, pCDFDuet-1, pCOLADuet-1, pRSFDuet-1, pETDuet-1 ![]() Novagen's pET vector manual (expression, toxcicity tips, etc) SLIC cloning, pGST-PP-GFP and pHIS-SUMO-GFP Ligation Independent Cloning (LIC) vectors from Mark Connelly: pMCSG10, pMCSG7, pMCSG17-20, pMCSG19, pMCSG21 Yeast 2-hybrid vectors (sundquist lab) pGADT7 and pGBKT7 PDEST14 pDEST15, pDEST17, pENTR/TEV/D-TOPO, MCS PENTRL1pLaclacZaL4, pENTRL1pLaclacZaR5, pENTR元pLactetL2, pENTRL5LacIL4, pENTRL5pLacSpecL2, pENTRR4pLacSpecR3
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