Blast 1. Blast 2 Low Complexity masking >GDB1_WHEAT MKTFLVFALIAVVATSAIAQMETSCISGLERPWQQQPLPPQQSFSQQPPFSQQQQQPLPQ QPSFSQQQPPFSQQQPILSQQPPFSQQQQPVLPQQSPFSQQQQLVLPPQQQQQQLVQQQI.

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Presentation transcript:

Blast 1

Blast 2

Low Complexity masking >GDB1_WHEAT MKTFLVFALIAVVATSAIAQMETSCISGLERPWQQQPLPPQQSFSQQPPFSQQQQQPLPQ QPSFSQQQPPFSQQQPILSQQPPFSQQQQPVLPQQSPFSQQQQLVLPPQQQQQQLVQQQI PIVQPSVLQQLNPCKVFLQQQCSPVAMPQRLARSQMWQQSSCHVMQQQCCQQLQQIPEQS RYEAIRAIIYSIILQEQQQGFVQPQQQQPQQSGQGVSQSQQQSQQQLGQCSFQQPQQQLG QQPQQQQQQQVLQGTFLQPHQIAHLEAVTSIALRTLPTMCSVNVPLYSATTSVPFGVGTG VGAY >GDB1_WHEAT SEG filtered MKTFLVFALIAVVATSAIAQMETSCISGLERPWXXXXXXXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXLNPCKVFLQQQCSPVAMPQRLARSQMWXXXXXXXXXXXXXXXXXXXXXXX RYEAIRAIIYSIIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXHQIAHLEAVTSIALRTLPTMCSVNVPLYSATTSVPFGVGTG VGAY

Low Complexity 2 >MTG8_HUMAN Q06455 MISVKRNTWRALSLVIGDCRKKGNFEYCQDRTEKHSTMPD SPVDVKTQSRLTPPTMPPPPTTQGAPRTSSFTPTTLTNGT SHSPTALNGAPSPPNGFSNGPSSSSSSSLANQQLPPACGA RQLSKLKRFLTTLQQFGNDISPEIGERVRTLVLGLVNSTL TIEEFHSKLQEATNFPLRPFVIPFLKANLPLLQRELLHCA RLAKQNPAQYLAQHEQLLLDASTTSPVDSSELLLDVNENG KRRTPDRTKENGFDREPLHSEHPSKRPCTISPGQRYSPNN GLSYQPNGLPHPTPPPPQHYRLDDMAIAHHYRDSYRHPSH RDLRDRNRPMGLHGTRQEEMIDHRLTDREWAEEWKHLDHL LNCIMDMVEKTRRSLTVLRRCQEADREELNYWIRRYSDAE DLKKGGGSSSSHSRQQSPVNPDPVALDAHREFLHRPASGY VPEEIWKKAEEAVNEVKRQAMTELQKAVSEAERKAHDMIT TERAKMERTVAEAKRQAAEDALAVINQQEDSSESCWNCGR KASETCSGCNTARYCGSFCQHKDWEKHHHICGQTLQAQQQ GDTPAVSSSVTPNSGAGSPMDTPPAATPRSTTPGTPSTIE TTPR Rat 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.