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Blast 1
Blast 2
Low Complexity masking>GDB1_WHEAT MKTFLVFALIAVVATSAIAQMETSCISGLERPWQQQPLPPQQSFSQQPPFSQQQQQPLPQQPSFSQQQPPFSQQQPILSQQPPFSQQQQPVLPQQSPFSQQQQLVLPPQQQQQQLVQQQIPIVQPSVLQQLNPCKVFLQQQCSPVAMPQRLARSQMWQQSSCHVMQQQCCQQLQQIPEQSRYEAIRAIIYSIILQEQQQGFVQPQQQQPQQSGQGVSQSQQQSQQQLGQCSFQQPQQQLGQQPQQQQQQQVLQGTFLQPHQIAHLEAVTSIALRTLPTMCSVNVPLYSATTSVPFGVGTGVGAY>GDB1_WHEAT SEG filteredMKTFLVFALIAVVATSAIAQMETSCISGLERPWXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLNPCKVFLQQQCSPVAMPQRLARSQMWXXXXXXXXXXXXXXXXXXXXXXXRYEAIRAIIYSIIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHQIAHLEAVTSIALRTLPTMCSVNVPLYSATTSVPFGVGTGVGAY
Low Complexity 2>MTG8_HUMAN Q06455 MISVKRNTWRALSLVIGDCRKKGNFEYCQDRTEKHSTMPDSPVDVKTQSRLTPPTMPPPPTTQGAPRTSSFTPTTLTNGTSHSPTALNGAPSPPNGFSNGPSSSSSSSLANQQLPPACGARQLSKLKRFLTTLQQFGNDISPEIGERVRTLVLGLVNSTLTIEEFHSKLQEATNFPLRPFVIPFLKANLPLLQRELLHCARLAKQNPAQYLAQHEQLLLDASTTSPVDSSELLLDVNENGKRRTPDRTKENGFDREPLHSEHPSKRPCTISPGQRYSPNNGLSYQPNGLPHPTPPPPQHYRLDDMAIAHHYRDSYRHPSHRDLRDRNRPMGLHGTRQEEMIDHRLTDREWAEEWKHLDHLLNCIMDMVEKTRRSLTVLRRCQEADREELNYWIRRYSDAEDLKKGGGSSSSHSRQQSPVNPDPVALDAHREFLHRPASGYVPEEIWKKAEEAVNEVKRQAMTELQKAVSEAERKAHDMITTERAKMERTVAEAKRQAAEDALAVINQQEDSSESCWNCGRKASETCSGCNTARYCGSFCQHKDWEKHHHICGQTLQAQQQGDTPAVSSSVTPNSGAGSPMDTPPAATPRSTTPGTPSTIETTPRRat apoptosis RP-8 AED…LQA goes from 62/599 to 6/83
Blast limit by taxon
Blast results
Blast aligns
EBI Blast
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
BlastN
• Do not use for protein coding.
• Distant relations will be saturated
• Use FASTA instead?
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
TblastN
• Yr protein query vs NA DB (Genbank)
• Required for EST search
• Finds unannotated ORFs
• SNPs
TblastX
• Searches yr NA (6-frame transl) vs DNA DB (6-frame transl).
• Fishing expedition
• 36x more CPU than simple blastN
More?
• NCBI blast site has excellent tutorial and FAQ
• Manual has relevant pages of hints, theory and examples.