blastp

Set subsequence: From To

Database nr swissprot prat yeast ecoli pdb Drosophila genome month Do CD-search

Limit by Entrez query

or select from (none) Viruses [ORGN] Archaea [ORGN] Bacteria [ORGN] Eukaryota [ORGN] Viridiplantae [ORGN] Fungi [ORGN] Metazoa [ORGN] Arthropoda [ORGN] Vertebrata [ORGN] Mammalia [ORGN] Rodentia [ORGN] Primates [ORGN] ------------------- Aeropyrum pernix [ORGN] Aquifex aeolicus [ORGN] Arabidopsis thaliana [ORGN] Bacillus subtilis [ORGN] Bos taurus [ORGN] Caenorhabditis elegans [ORGN] Danio rerio [ORGN] Dictyostelium discoideum [ORGN] Drosophila melanogaster [ORGN] Escherichia coli [ORGN] Gallus gallus [ORGN] Homo sapiens [ORGN] Human immunodeficiency virus type 1 [ORGN] Methanococcus jannaschii [ORGN] Mus musculus [ORGN] Oryctolagus cuniculus [ORGN] Oryza sativa [ORGN] Ovis aries [ORGN] Plasmodium falciparum [ORGN] Rattus norvegicus [ORGN] Saccharomyces cerevisiae [ORGN] Schizosaccharomyces pombe [ORGN] Simian immunodeficiency virus [ORGN] Synechocystis PCC6803 [ORGN] Takifugu rubripes [ORGN] Xenopus laevis [ORGN] Zea mays [ORGN]

Composition based statistics

Choose Filter:
Low complexity Mask for lookup table only Mask lower case

Expect

Word Size 2 3

Matrix PAM30 PAM70 BLOSUM80 BLOSUM62 BLOSUM45

Gap cost 11 1 9 2 8 2 7 2 12 1 10 1

PSSM

Other Advanced option

PHI pattern

Show Alignment PSSM Bioseq Format HTML Plain text ASN.1 XML

Number of descriptions 0 10 50 100 250 500 1000

Number of alignments 0 10 50 100 250 500 1000

Alignment view Pairwise query-anchored with identities query-anchored without identities flat query-anchored with identities flat query-anchored without identities

Format for PSI-BLAST with inclusion threshhold

Layout One Window Two Windows

Format on the result page None At the top At the bottom

Autoformat Off Semi-auto Full-auto

Send result by e. mail

blastn

Set subsequence: From To

Database nr est est_human est_mouse est_others gss htgs pat yeast mito vector ecoli pdb Drosophila genome month alu dbsts

Choose filter: Low complexity Human repeats Mask for lookup table only Mask lower case

Expect Word size 7 11 15

Other advanced option

Format type HTML Plain text ASN.1 XML

Number of descriptions 0 10 50 100 250 500 1000

Number of alignments 0 10 50 100 250 500 1000

Alignment view Pairwise query-anchored with identities query-anchored without identities flat query-anchored with identities flat query-anchored without identities

Layout One Window Two Windows

Formatting options on page with results None At the top At the bottom

Autoformat Off Semi-auto Full-auto

Send results by e-mail

Translated BLAST

Choose program TRANSLATED query - PROTEIN database [blastx] PROTEIN query - TRANSLATED database [tblastn] TRANSLATED query - TRANSLATED database [tblastx]

Set subsequence: From To

Choose database nr swissprot prat yeast ecoli pdb Drosophila genome month

Genetic code Standard (1) Vertebrate Mitochondrial (2) Yeast Mitochondrial (3) Mold Mitochondrial; ... (4) Invertebrate Mitochondrial (5) Ciliate Nuclear; ... (6) Echinoderm Mitochondrial (9) Euplotid Nuclear (10) Bacterial (11) Alternative Yeast Nuclear (12) Ascidian Mitochondrial (13) Flatworm Mitochondrial (14) Blepharisma Macronuclear (15)

Choose filter Low complexity Mask for lookup table only Mask lower case

Expect

Word Size 2 3

Matrix PAM30 PAM70 BLOSUM80 BLOSUM62 BLOSUM45

Gap cost 11 1 9 2 8 2 7 2 12 1 10 1

Other advanced option

Format HTML Plain text ASN.1 XML

Number of descriptions 0 10 50 100 250 500 1000

Number of alignments 0 10 50 100 250 500 1000

Alignment view Pairwise query-anchored with identities query-anchored without identities flat query-anchored with identities flat query-anchored without identities Hit Table

Layout One Window Two Windows

Formatting options on page with results None At the top At the bottom

Autoformat Off Semi-auto Full-auto

Send results by e-mail

fasta

Fasta program
fasta: protein or DNA query vs similar db (FASTA release 3.0) tfasta: protein query vs translated DNA db fastx: DNA query (translated, 3 frames) vs protein db (frameshifts only between codons) tfastx: protein query vs translated DNA db (frameshifts only between codons) fasty = fastx + frameshifts anywhere tfasty = tfastx + frameshifts anywhere fastf: mixed peptide seq vs protein db (modified algorithm) tfastf: mixed peptide seq vs translated DNA db (modified algorithm) fasts: several short peptide seq vs protein db (modified algorithm) tfasts: several short peptide seq vs translated DNA db (modified algorithm)

Break long library sequences into blocks (-N)

Display more information about the library sequence in the alignment (-L)

Is it a DNA or protein sequence (-n)
DNA protein

Write out the sequence identifier, superfamily number, and similarity scores to this file (-R)

Lower case filtering (-S)

OPTCUT : the threshold for optimization. (-c)

Penalty for gap initiation (-12 by default for fasta with proteins, -16 for DNA) (-f)

Penalty for gap extention (-2 by default for fasta with proteins, -4 for DNA) (-g)

Maximal expectation value threshold for displaying scores and alignments (-E)

Minimal expectation value threshold for displaying scores and alignments (-F)

Reward for a nucleotid match (-r)

Penalty for a nucleotid mismatch (-r)

Scoring matrix file (-s)
BLOSUM50 BLOSUM62 BLOSUM80 PAM20 PAM40 PAM120 PAM250 MDM_10 MDM_20 MDM_40

Penalty for a match to 'X' (independently of the PAM matrix) (-x)

Penalty for frameshift between codon (fast[xy]/tfast[xy])(-h)

Penalty for frameshift within a codon (fasty/tfasty)(-j)

Search only the three forward frames (tfasta) (-3)

Reverse complement the query sequence (all tfasta) (-i)

Use genetic code for translation (tfasta/tfast[xy]/fast[xy]) (-t)
1: Standard 2: Vertebrate Mitochondrial 3: Yeast Mitochondrial 4: Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma 5: Invertebrate Mitochondrial 6: Ciliate Macronuclear and Dasycladacean 9: Echinoderm Mitochondrial 10: Euplotid Nuclear 11: Bacterial 12: Alternative Yeast Nuclear 13: Ascidian Mitochondrial 14: Flatworm Mitochondrial 15: Blepharisma Macronuclear

band-width used for optimization (-y)

unlimited Smith-Waterman alignment for DNA (-A)

no limited optimization (-o)

Specify statistical calculation. (-z)
-1: turn off statistics 0: no correction of library sequebce length 1: weigthed regression against the length of the library sequence 2: maximum likelihood estimates of Lambda abd K 3: Altschul-Gish parameters 4: Variation1 of 1 5: Variation2 of 1

Estimate stat parameters from shuffled copies of each library sequence (-z)

No histogram (-H)

number of similarity scores to be shown (-b)

number of alignments to be shown (-d)

HTML output (-m)

Alternate display of matches and mismatches in alignments
0 [: identities] [. conservative repl] [ non-conserv repl] 1: [ identities] [x conservative repl] [X non-conserv repl] 2: [. identities] [res mismatch] - don't display the 2nd seq 3: writes a file of library sequences in FASTA format 4: displays a graph of the alignment 9: 0 + percent identity + coordinates 10: output more information

sequences ranked by the z-score based on the init1 score (-1)

Show normalize score as (-B)
z-score bit-score

both sequences are shown in their entirety in alignments (fasta only) (-a)

output line length for sequence alignments (max. 200) (-w)

Start numbering the aligned sequences at position x1 x2 (2 numbers) (-X)

Protein Database
sptrnrdb: non-redundant SWISS-PROT + TrEMBL swissprot (last release + updates) swissprot release swissprot_new: updates pir: Protein Information Resource nrprot: NCBI non-redundant Genbank CDS translations+PDB+Swissprot+PIR nrprot_month: NCBI month non-redundant Genbank CDS translations+PDB+Swissprot+PIR genpept: Genbank translations (last rel. + upd.) genpept_new: genpept updates gpbct: genpept bacteries gppri: primates gpmam: other mammals gprod: rodents gpvrt: other vertebrates gpinv: invertebrates gppln: plants (including yeast) gpvrl: virus gpphg: phages gpsts: STS gpsyn: synthetic gppat: patented gpuna: unatotated gphtg: GS (high throughput Genomic Sequencing) nrl3d: sequences from PDB prodom: protein domains sbase: annotated domains sequences

Nucleotid Database
embl: Embl last release + updates embl_new: Embl updates genbank: Genbank last release + updates genbank_new: Genbank updates gbbct: genbank bacteria gbpri: primates gbmam: other mammals gbrod: rodents gbvrt: other vertebrates gbinv: invertebrates gbpln: plants (including yeast) gbvrl: virus gbphg: phages gbest: EST (Expressed Sequence Tags) gbsts: STS (Sequence Tagged sites) gbsyn: synthetic gbpat: patented gbuna: unannotated gbgss: Genome Survey Sequences gbhtg: GS (high throughput Genomic Sequencing) imgt: ImMunoGeneTics borrelia: Borrelia burgdorferi complete genome ecoli: Escherichia Coli complete genome genitalium: Mycoplasma Genitalium complete genome pneumoniae: Mycoplasma Pneumoniae complete genome pylori: Helicobacter Pylori complete genome subtilis: Bacillus Subtilis complete genome tuberculosis: Mycobacterium tuberculosis complete genome Yersinia pestis unfinished genome yeast: Yeast chromosomes

ktup : sensitivity and speed of the search (protein:2, DNA:6)