blast 1. blast 2 low complexity masking >gdb1_wheat...

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.