Cinara cedri blast server Job title Email address Program selection Programblastn (nucleotide vs nucleotide)blastp (protein vs protein)blastx (nucleotide vs protein)tblastn (protein vs nucleotide)tblastx (nucleotide vs nucleotide, but at protein level) Search typeHighly similar sequences (megablast)More dissimilar sequences (discontiguous megablast)Somewhat similar sequences (blastn) Search typeNormal blastpPSI-BLAST (Position-Specific Iterated BLAST)PHI-BLAST (Pattern Hit Initiated BLAST)DELTA-BLAST (Domain Enhanced Lookup Time Accelerated BLAST) PSI-BLAST, PHI-BLAST and DELTA-BLAST can be used to find distantly related sequences Query sequence Paste your sequence FASTA format. Length is limited to 20Mb Or select a file FASTA format. File size is limited to 20Mb Query genetic codeStandardVertebrate MitochondrialYeast MitochondrialMold Mitochondrial; ...Invertebrate MitochondrialCiliate Nuclear; ...Echinoderm MitochondrialEuplotid NuclearBacteria and ArchaeaAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma Macrouclear Databank selection Databank typePublic databankPersonal databank Databank typePublic databankPersonal databank Select a personal databank (FASTA format) File size is limited to 20Mb DatabankCinara cedri assembly CINCED3Cinara cedri assembly CINCED3 annotation IGEPP CDSCinara cedri assembly CINCED3 annotation IGEPP transcriptsCinara cedri assembly CINCED3 annotation NCBI CDSCinara cedri assembly CINCED3 annotation NCBI transcriptsCinara cedri assembly CINCED3 annotation IGEPP proteinsCinara cedri assembly CINCED3 annotation NCBI proteins Databank genetic codeStandardVertebrate MitochondrialYeast MitochondrialMold Mitochondrial; ...Invertebrate MitochondrialCiliate Nuclear; ...Echinoderm MitochondrialEuplotid NuclearBacteria and ArchaeaAlternative Yeast NuclearAscidian MitochondrialFlatworm MitochondrialBlepharisma Macrouclear General parameters Expect1e-201e-100.00010.010.11101001000 The statistical significance threshold for reporting matches. Lowest values are the most stringent. Word size23 The length of the seed that initiates an alignment. Word size71115 The length of the seed that initiates an alignment. Word size16202428324864128256 The length of the seed that initiates an alignment. Word size1112 The length of the seed that initiates an alignment. Max target sequences1050100250500100050001000020000 Maximum number of aligned sequences to display Scoring parameters Matrix1,-21,-31,-42,-34,-51,-1 First number is the reward when two aligned nucleotides match. Second number is the penalty when two aligned nucleotides are different. Matrix1,-21,-31,-42,-34,-51,-1 First number is the reward when two aligned nucleotides match. Second number is the penalty when two aligned nucleotides are different. MatrixPAM30PAM70BLOSUM80BLOSUM62BLOSUM45 Substitution matrix for scoring any pair of residues. BLOSUM45 or PAM70 are for more divergent sequences. BLOSUM80 or PAM30 are for less divergent sequences. Gap costsCreation: 12 Extension: 8Creation: 6 Extension: 5Creation: 5 Extension: 5Creation: 4 Extension: 5Creation: 3 Extension: 5Creation: 4 Extension: 4Creation: 2 Extension: 4Creation: 0 Extension: 4Creation: 3 Extension: 3Creation: 6 Extension: 2Creation: 5 Extension: 2Creation: 4 Extension: 2Creation: 3 Extension: 2Creation: 2 Extension: 2Creation: 1 Extension: 2Creation: 0 Extension: 2Creation: 4 Extension: 1Creation: 3 Extension: 1Creation: 2 Extension: 1Creation: 1 Extension: 1 Penalties when opening and extending a gap in each alignment. Gap costsCreation: 13 Extension: 3Creation: 12 Extension: 3Creation: 11 Extension: 3Creation: 10 Extension: 3Creation: 15 Extension: 2Creation: 14 Extension: 2Creation: 13 Extension: 2Creation: 12 Extension: 2Creation: 9 Extension: 2Creation: 8 Extension: 2Creation: 7 Extension: 2Creation: 6 Extension: 2Creation: 5 Extension: 2Creation: 19 Extension: 1Creation: 18 Extension: 1Creation: 17 Extension: 1Creation: 16 Extension: 1Creation: 12 Extension: 1Creation: 11 Extension: 1Creation: 10 Extension: 1Creation: 9 Extension: 1Creation: 8 Extension: 1 Penalties when opening and extending a gap in each alignment. Compositional adjustmentsNo adjustmentComposition-based statisticsConditional compositional score matrix adjustmentUniversal compositional score matrix adjustment Matrix adjustment method to compensate for amino acid composition of sequences. Compositional adjustmentsNo adjustmentComposition-based statistics Matrix adjustment method to compensate for amino acid composition of sequences. Filters and masking Low complexity regions Mask off segments of the query sequence that have low compositional complexity. Soft masking Mask only when finding alignment seeds, not during extension. Mask lower case letters Filter regions in lower case in query sequence. PSI-BLAST and PHI-BLAST PSI-BLAST threshold Set the statistical significance threshold to include a sequence in the model used by PSI-BLAST to create the PSSM on the next iteration. DELTA-BLAST threshold Set the statistical significance threshold to include a domain in the model used by DELTA-BLAST to create the PSSM . Iteration number Number of iterations Pseudocount If zero is specified, then the parameter is automatically determined through a minimum length description principle (PMID 19088134). Upload PSSM Upload a Position Specific Score Matrix (PSSM) that you previously downloaded from a PSI-BLAST iteration. You may search a different database than that used to generate the PSSM, but you must use the same query. PHI-BLAST pattern Enter a PHI pattern (PROSITE format) to start the search. PHI-BLAST may perform better than simple pattern searching because it filters out false positives (pattern matches that are probably random and not indicative of homology). Discontiguous Word Options Template lengthNone161821 Total number of bases in a seed that ignores some positions. Template typeCodingMaximalTwo templates Specifies which bases are ignored in scanning the database.