PsiBLAST User Manual
Contents
1. Lower EXPECT thresholds are more stringent leading to fewer chance matches being reported Expect inclusion This parameter has the same statistical meaning as explained before The value given here is the threshold to report a match from one iteration to the next iteration Date 14 09 07 Manuel_psiBLAST_en Page 2 4 Matrix A key element in evaluating the quality of a pairwise sequence alignment is the substitution matrix which assigns a score for aligning any possible pair of residues The matrix used in aBLAST search can be changed depending on the type of sequences you are searching with see the BLAST Frequently Asked Questions Substitution Matrix A substitution matrix containing values proportional to the probability that amino acid i mutates into amino acid j for all pairs of amino acids The PAM family e PAM matrices are based on global alignments of closely relatedproteins e The PAM1 is the matrix calculated from comparisons of sequences with no more than 1 divergence e Other PAM matrices are extrapolated from PAM1 The BLOSUM family e BLOSUM matrices are based on local alignments e BLOSUM 62 is a matrix calculated from comparisons of sequences with no less than 62 divergence e All BLOSUM matrices are based on observed alignments they are not extrapolated from comparisons of closely related proteins e BLOSUM 62 is the default matrix in BLAST 2 0 Though it is tailored for comp2. Psi BLAST User Manual Table des matieres TAU OIG ONY enesenn a atalino teendstcl cadetet ae cea tel ew ntntbogor area eneadieitee Is Parmele Senee cic Dy ate ant a a a N ae Piste Databank si eee 2 SI bt eC ETO ROT ree PRT eC ee rr nee SEN RCE er are ener ne Tener EN 2 Expect men On e E EE 2 AEE EE E E E A E E E A E cota E E E E A A E E E A aas 3 SEO PE ea T T 3 Me re Ua NRTA mimber of pasie Seena aean ST E EAR A E ANET N ANE AR EES 4 Eea i E E E E AEE E E E E EE E E E E E E A EE E 4 Introduction PSI BLAST Position Specific Iterative BLAST is a protein BLAST search that uses a PSSM position specific scoring matrix as a query instead of an individual sequence PSI BLAST refers to a feature of BLAST 2 0 in which a profile or position specific scoring matrix PSSM is constructed automatically from a multiple alignment of the highest scoring hits in an initial BLAST search The PSSM is generated by calculating position specific scores for each position in the alignment Highly conserved positions receive high scores and weakly conserved positions receive scores near zero The profile is used to perform a second etc BLAST search and the results of each iteration used to refine the profile This iterative searching strategy results in increased sensitivity Reference Altschul S F Gish W Miller W Myers E W Lipman D J 1990 Basic local alignment search tool J Mol Biol 215 403 410 Date 14 09 07 Manu
3. arisons of moderately distant proteins it performs well in detecting closer relationships A search for distant relatives may be more sensitive with a different matrix Note If you re not sure about your matrix choice use BLOSUM62 SEG Filter This function mask off segments of the query sequence that have low compositional complexity as determined by the SEG program of Wootton and Federhen Computers and Chemistry 1993 Filtering can eliminate statistically significant but biologically uninteresting reports from the blast output e g hits against common acidic basic or proline rich regions leaving the more biologically interesting regions of the query sequence available for specific matching against database sequences Filtering is only applied to the query sequence or its translation products not to database sequences Default filtering is SEG for psi BLAST program SEG A program for filtering low complexity regions in amino acid sequences Residues that have been masked are represented as X in an alignment Date 14 09 07 Manuel_psiBLAST_en Page 3 4 Maximum number of passes It is the maximum number of passes to use during the Psi blast s research in multipass Gap costs Increasing the Gap Costs and Lambda ratio will result in alignments which decrease the number of Gaps introduced Date 14 09 07 Manuel_psiBLAST_en Page 4 4
4. el_psiBLAST_en Page 1 4 Parameters Proteic Databank Select a sequence databank versus which theresearch will be launched e NR Non redundant Proteicsequences collection maintained at NCBI e Uniprot Universal Protein Resource Proteic sequences collection merging informations from 3 databanks Swiss Prot TTEMBL and PIR e PIR Protein Information Ressource Proteic sequences collection maintained by Georgetown Universty Medical Center USA e SwissProt Non redundant Proteic sequences collection produced by sequencing maintained by Expasy Switzerland e Genpept GenPept is produced by parsing the corresponding GenBank NCBI release for translated coding regions as definedin the GenBank FEATURES section of each sequence e RefSeq Protein The RefSeq Reference Sequence collection provide a comprehensive integrated non redundant set of sequences including genomic DNA transcript RNA and protein products This databank is managd by NCBI e PDB Protein Data Bank protein with known 3D structure sequences Expect This setting specifies the statistical significance threshold for reporting matches against database sequences The default value 10 means that 10 such matches are expected to be found merely by chance according to the stochastic model of Karlin and Altschul 1990 If the statistical significance ascribed to a match is greater than the EXPECT threshold the match will not be reported
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