Genotyping

This tool helps identify the genotype of a viral sequence. A window is slid along the query sequence and each window is compared by BLAST to each of the reference sequences for a particular virus. This approach is especially useful for the analysis of recombinant sequences. (Try an example).

Select:

Add/remove reference sequences as Accession\|subtype:		Enter local reference sequences as FASTA:
AF004885\|A1 AF069670\|A1 M62320\|A1 U51190\|A1 AF286237\|A2 AF286238\|A2 AF286240\|A2 AF286241\|A2 U21135\|B M17451\|B U63632\|B K03455\|B U52953\|C U46016\|C AF443091\|C AF110967\|C AF067155\|C M27323\|D U88822\|D U88824\|D K03454\|D AJ249238\|F1 AF075703\|F1 AF077336\|F1 AF005494\|F1 AJ249236\|F2 AJ249237\|F2 AF061641\|G AF061642\|G AF084936\|G U88826\|G AF005496\|H AF190127\|H AF190128\|H AF082394\|J AF082395\|J AJ249239\|K AJ249235\|K AJ006022\|N AJ271370\|N AJ302646\|O AJ302647\|O L20571\|O L20587\|O AY046058\|U AF457101\|U AF286236\|U AF197340\|CRF01 AF197341\|CRF01 U51188\|CRF01 U54771\|CRF01 L39106\|CRF02 AF107770\|CRF02 AF063224\|CRF02 AJ286133\|CRF02 AF193276\|CRF03 AF193277\|CRF03 AF119819\|CRF04 AF119820\|CRF04 AF049337\|CRF04 AF076998\|CRF05 AF193253\|CRF05 AF064699\|CRF06 AJ288981\|CRF06 AJ288982\|CRF06 AJ245481\|CRF06 AF503396\|CRF07 AF286226\|CRF07 AF286230\|CRF07 AF286229\|CRF08 AY008715\|CRF08 AY008716\|CRF08 AY008717\|CRF08 AY093603\|CRF09 AY093604\|CRF09 AY093605\|CRF09 AY093607\|CRF09 AF289548\|CRF10 AF289549\|CRF10 AF289550\|CRF10 AF492623\|CRF11 AF492624\|CRF11 AJ291718\|CRF11 AJ291719\|CRF11 AJ291720\|CRF11 AF179368\|CRF11 AY371149\|CRF11 AY371150\|CRF11 AY371151\|CRF11 AY371152\|CRF11 AY371153\|CRF11 AY037279\|CRF12 AF385934\|CRF12 AF385935\|CRF12 AF385936\|CRF12 AF408629\|CRF12 AF408630\|CRF12 AF460972\|CRF13 AF460974\|CRF13 AY371154\|CRF13 AF450096\|CRF14 AF450097\|CRF14 AF423756\|CRF14 AF423757\|CRF14 AF423758\|CRF14 AF423759\|CRF14 AF516184\|CRF15 AF529572\|CRF15 AF529573\|CRF15 AF530576\|CRF15 AF457060\|CRF16 AF286239\|CRF16 AF115393\|CPZ AF103818\|CPZ AJ271369\|CPZ U42720\|CPZ X52154\|CPZ

Enter your query sequence as Accession/GI or FASTA



Enter window size:		Select background color:
Enter increment step:		Similarity threshold (%):
		Table output only:

Please send questions and comments to info@ncbi.nlm.nih.gov