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Blast 1
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Blast 2
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Low Complexity masking>GDB1_WHEAT MKTFLVFALIAVVATSAIAQMETSCISGLERPWQQQPLPPQQSFSQQPPFSQQQQQPLPQQPSFSQQQPPFSQQQPILSQQPPFSQQQQPVLPQQSPFSQQQQLVLPPQQQQQQLVQQQIPIVQPSVLQQLNPCKVFLQQQCSPVAMPQRLARSQMWQQSSCHVMQQQCCQQLQQIPEQSRYEAIRAIIYSIILQEQQQGFVQPQQQQPQQSGQGVSQSQQQSQQQLGQCSFQQPQQQLGQQPQQQQQQQVLQGTFLQPHQIAHLEAVTSIALRTLPTMCSVNVPLYSATTSVPFGVGTGVGAY>GDB1_WHEAT SEG filteredMKTFLVFALIAVVATSAIAQMETSCISGLERPWXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLNPCKVFLQQQCSPVAMPQRLARSQMWXXXXXXXXXXXXXXXXXXXXXXXRYEAIRAIIYSIIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHQIAHLEAVTSIALRTLPTMCSVNVPLYSATTSVPFGVGTGVGAY
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Low Complexity 2>MTG8_HUMAN Q06455 MISVKRNTWRALSLVIGDCRKKGNFEYCQDRTEKHSTMPDSPVDVKTQSRLTPPTMPPPPTTQGAPRTSSFTPTTLTNGTSHSPTALNGAPSPPNGFSNGPSSSSSSSLANQQLPPACGARQLSKLKRFLTTLQQFGNDISPEIGERVRTLVLGLVNSTLTIEEFHSKLQEATNFPLRPFVIPFLKANLPLLQRELLHCARLAKQNPAQYLAQHEQLLLDASTTSPVDSSELLLDVNENGKRRTPDRTKENGFDREPLHSEHPSKRPCTISPGQRYSPNNGLSYQPNGLPHPTPPPPQHYRLDDMAIAHHYRDSYRHPSHRDLRDRNRPMGLHGTRQEEMIDHRLTDREWAEEWKHLDHLLNCIMDMVEKTRRSLTVLRRCQEADREELNYWIRRYSDAEDLKKGGGSSSSHSRQQSPVNPDPVALDAHREFLHRPASGYVPEEIWKKAEEAVNEVKRQAMTELQKAVSEAERKAHDMITTERAKMERTVAEAKRQAAEDALAVINQQEDSSESCWNCGRKASETCSGCNTARYCGSFCQHKDWEKHHHICGQTLQAQQQGDTPAVSSSVTPNSGAGSPMDTPPAATPRSTTPGTPSTIETTPRRat apoptosis RP-8 AED…LQA goes from 62/599 to 6/83
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Blast limit by taxon
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Blast results
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Blast aligns
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EBI Blast
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BlastP
• BlastP use low complexity masking
• Default Blosum62
• PAM30/Blosum90 recent divergence, good for motifs
• PAM250/Blosum30 distant relats. Good for long weak matches
• If your seq is CDS translate before blast
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BlastN
• Do not use for protein coding.
• Distant relations will be saturated
• Use FASTA instead?
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BlastX
• NA query (6 frame transl) vs Protein DB
• Swissprot for good annotation
• nr for comprehensive
• Use to check for frameshifts
• Use low complex masking
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TblastN
• Yr protein query vs NA DB (Genbank)
• Required for EST search
• Finds unannotated ORFs
• SNPs
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TblastX
• Searches yr NA (6-frame transl) vs DNA DB (6-frame transl).
• Fishing expedition
• 36x more CPU than simple blastN
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More?
• NCBI blast site has excellent tutorial and FAQ
• Manual has relevant pages of hints, theory and examples.