BLASTP 2.0MP-WashU [09-Sep-1999] [irix6-r10k-b64 12:19:05 09-Sep-1999] Copyright (C) 1996-1999 Washington University, Saint Louis, Missouri USA. All Rights Reserved. Reference: Gish, W. (1996-1999) http://blast.wustl.edu Usage: BLASTP database queryfile [options] Valid BLASTP options: E, S, E2, S2, W, T, X, M, Y, Z, H, V and B -sump use Karlin-Altschul "Sum" statistics* -poissonp use Poisson statistics to evaluate multiple HSPs -compat1.4 revert to BLAST version 1.4 behavior (with bug fixes) -compat1.3 revert to BLAST version 1.3 behavior (with bug fixes) -filter method (e.g., methods of "seg", "xnu", or "seg+xnu") -echofilter display the filtered query sequence -hitdist # max. distance between word hits for 2-hit BLAST (default 0) -wink # generate neighborhood words every wink-th position (default 1) -stats collect word-hit statistics (consumes a little additional cpu time) -ctxfactor # base statistics on this number of independent contexts or reading frames -nogap turn off gapped alignment method, report only ungapped HSPs -gapE # expectation threshold of ungapped HSP sets for seeding gapped alignments -gapall perform gapped alignment procedure on all ungapped HSPs (slower) -gapE2 # expectation threshold for saving individual gapped alignments (GSPs) -gapS2 # cutoff score for saving individual gapped alignments -gapW # band width (full, not half) for gapped alignment procedure -postsw perform full Smith-Waterman before output (BLASTP only) -olf # max. fractional length of overlap for HSP consistency -golf # max. fractional length overlap for GSP consistency -gapdecayrate # -span2 discard HSPs spanned on both query and subject by a better HSP* -span1 discard HSPs spanned on query, subject or both by a better HSP -span do not discard HSPs spanned by other, better HSPs -prune do not prune insignificant HSPs from the output lists -edegrade # only show HSP combos within this factor of the best combo -consistency turn off HSP consistency rules for statistics -nonnegok make all non-negative expected scores a non-FATAL error -novalidctxok make no valid contexts a non-FATAL error -hspsepqmax max. separation allowed between HSPs along query -hspsepsmax max. separation allowed between HSPs along subject -gapsepqmax max. separation allowed between GSPs along query -gapsepsmax max. separation allowed between GSPs along subject -matrix matrixfile specify a scoring matrix file -altscore qc,sc,score qc and sc may be letters or "all"; score may be #, "min", "max", or "na" -hspmax # max. no. of HSPs saved/reported per subject sequence, default 1000 -qoffset # adjust query coordinate numbering by this amount -nwstart # start generating neighborhood words here in query -nwlen # generate neighborhood words over this distance in query -dbrecmin # starting database record number to search -dbrecmax # ending database record number to search -gi display gi identifiers, when available -noseqs do not display sequence alignments -- abbreviated output -qtype exit non-zero if query seems to be of wrong type -qres exit non-zero if query contains an invalid residue code -sort_by_pvalue -sort_by_count -sort_by_highscore -sort_by_totalscore -cpus # no. of processors to utilize on multi-processor systems -mmio do not use memory-mapped I/O (usually slower) -notes suppress informatory messages -warnings suppress warning messages -errors suppress non-fatal error messages -abortonerror abort (and possibly dump core) on a non-fatal error -abortonfatal abort (and possibly dump core) on a fatal error -progress # report progress of search at least this often (seconds) -o fname write output to file named "fname", instead of stdout -asn1 produce ASN.1 "print-value" output (currently broken) -asn1bin produce binary-encoded ASN.1 output (currently broken) *Default program behavior
BLASTN 2.0MP-WashU [09-Sep-1999] [irix6-r10k-b64 12:19:05 09-Sep-1999] Copyright (C) 1996-1999 Washington University, Saint Louis, Missouri USA. All Rights Reserved. Reference: Gish, W. (1996-1999) http://blast.wustl.edu Notice: this program and its default parameter settings are optimized to find nearly identical sequences rapidly. To identify weak similarities encoded in nucleic acid, use BLASTX, TBLASTN or TBLASTX. Usage: BLASTN database queryfile [options] Valid BLASTN options: E, S, E2, S2, W, T, X, M, N, Y, Z, H, V and B -sump use Karlin-Altschul "Sum" statistics* -poissonp use Poisson statistics to evaluate multiple HSPs -compat1.4 revert to BLAST version 1.4 behavior (with bug fixes) -compat1.3 revert to BLAST version 1.3 behavior (with bug fixes) -top search only the top strand of the query -bottom search only the bottom strand of the query -filter method (e.g., methods of "seg", "xnu", or "seg+xnu") -echofilter display the filtered query sequence -hitdist # max. distance between word hits for 2-hit BLAST (default 0) -wink # generate neighborhood words every wink-th position (default 1) -stats collect word-hit statistics (consumes a little additional cpu time) -ctxfactor # base statistics on this number of independent contexts or reading frames -nogap turn off gapped alignment method, report only ungapped HSPs -gapE # expectation threshold of ungapped HSP sets for seeding gapped alignments -gapall perform gapped alignment procedure on all ungapped HSPs (slower) -gapE2 # expectation threshold for saving individual gapped alignments (GSPs) -gapS2 # cutoff score for saving individual gapped alignments -gapW # band width (full, not half) for gapped alignment procedure -postsw perform full Smith-Waterman before output (BLASTP only) -olf # max. fractional length of overlap for HSP consistency -golf # max. fractional length overlap for GSP consistency -gapdecayrate # -span2 discard HSPs spanned on both query and subject by a better HSP* -span1 discard HSPs spanned on query, subject or both by a better HSP -span do not discard HSPs spanned by other, better HSPs -prune do not prune insignificant HSPs from the output lists -edegrade # only show HSP combos within this factor of the best combo -consistency turn off HSP consistency rules for statistics -nonnegok make all non-negative expected scores a non-FATAL error -novalidctxok make no valid contexts a non-FATAL error -hspsepqmax max. separation allowed between HSPs along query -hspsepsmax max. separation allowed between HSPs along subject -gapsepqmax max. separation allowed between GSPs along query -gapsepsmax max. separation allowed between GSPs along subject -matrix matrixfile specify a scoring matrix file -altscore qc,sc,score qc and sc may be letters or "all"; score may be #, "min", "max", or "na" -hspmax # max. no. of HSPs saved/reported per subject sequence, default 1000 -qoffset # adjust query coordinate numbering by this amount -dbrecmin # starting database record number to search -dbrecmax # ending database record number to search -gi display gi identifiers, when available -noseqs do not display sequence alignments -- abbreviated output -qtype exit non-zero if query seems to be of wrong type -qres exit non-zero if query contains an invalid residue code -sort_by_pvalue -sort_by_count -sort_by_highscore -sort_by_totalscore -cpus # no. of processors to utilize on multi-processor systems -mmio do not use memory-mapped I/O (usually slower) -notes suppress informatory messages -warnings suppress warning messages -errors suppress non-fatal error messages -abortonerror abort (and possibly dump core) on a non-fatal error -abortonfatal abort (and possibly dump core) on a fatal error -progress # report progress of search at least this often (seconds) -o fname write output to file named "fname", instead of stdout -asn1 produce ASN.1 "print-value" output (currently broken) -asn1bin produce binary-encoded ASN.1 output (currently broken) *Default program behavior
BLASTX 2.0a8MP-WashU [25-Feb-1997] [Build 20:41:27 Feb 25 1997] Copyright (C) 1995-1997 by Warren R. Gish. All Rights Reserved. Reference: Gish, Warren (1994-1997). unpublished. Gish, Warren and David J. States (1993). Identification of protein coding regions by database similarity search. Nat. Genet. 3:266-72. Notice: statistical significance is estimated under the assumption that the equivalent of one entire reading frame in the query sequence codes for protein and that significant alignments will involve only coding reading frames. Usage: BLASTX database queryfile [options] Valid BLASTX options: E, S, E2, S2, W, T, X, M, C, Y, Z, H, V and B -sump (Karlin-Altschul "Sum" statistics, the default) -poissonp (Poisson statistics) -compat1.4 (revert to BLAST version 1.4 behavior, approximately) -compat1.3 (revert to BLAST version 1.3 behavior, approximately) -top (search only the top strand of the query) -bottom (search only the bottom strand of the query) -filter method (e.g., methods of "seg", "xnu", or "seg+xnu") -echofilter (display the filtered query sequence) -stats conserve cpu time by not collecting statistics -ctxfactor # base statistics on this no. of independent contexts -gap turn off gapped alignment, reporting just BLAST alignments -gapall run gapped alignment procedure on all BLAST HSPs (slower) -gapw # set the band width for gapped subalignments -gapS2 # set S2 cutoff score for gapped subalignments -gapdecayrate # -olf # max. fractional length of overlap for HSP consistency -golf # max. fractional length overlap for gapped alignment consistency -span2 (the default) -span1 -span -prune -edegrade # only show HSP combos within this factor of the best combo -consistency (turn off HSP consistency statistics) -hspsepqmax max. separation along query sequence between HSPs -gapsepqmax max. separation along query between gapped alignments -hspsepsmax max. separation along subject sequence between HSPs -gapsepsmax max. separation along subject between gapped alignments -matrix matrixfile (specify a scoring matrix file) -altscore "qc sc score" (qc or sc may be "any", score may be "min", "max", or "na") -hspmax # (max. no. of HSPs per db seq, default 1000) -qoffset # (adjust query coordinate numbering by this amount) -nwstart # (start generating neighborhood words here) -nwlen # (generate neighborhood words for this length) -dbrecmin # (starting database record number) -dbrecmax # (ending database record number) -gi (display gi identifiers, when available) -noseqs (do not display sequence alignments -- abbreviated output) -qtype (exit non-zero if query seems to be of wrong type) -qres (exit non-zero if query contains an invalid residue code) -sort_by_pvalue -sort_by_count -sort_by_highscore -sort_by_totalscore -mmio (do not use memory-mapped I/O) -warnings (suppress warning messages) -progress # report progress of search at least this often (seconds) -asn1 (produce ASN.1 "print-value" output) -asn1bin (produce binary-encoded ASN.1 output)
TBLASTN 2.0MP-WashU [09-Sep-1999] [irix6-r10k-b64 12:19:05 09-Sep-1999] Copyright (C) 1996-1999 Washington University, Saint Louis, Missouri USA. All Rights Reserved. Reference: Gish, W. (1996-1999) http://blast.wustl.edu Notice: statistical significance is estimated under the assumption that the equivalent of one entire reading frame of the database codes for protein and that significant alignments will involve only coding reading frames. Usage: TBLASTN database queryfile [options] Valid TBLASTN options: E, S, E2, S2, W, T, X, M, C, Y, Z, H, V and B -sump use Karlin-Altschul "Sum" statistics* -poissonp use Poisson statistics to evaluate multiple HSPs -compat1.4 revert to BLAST version 1.4 behavior (with bug fixes) -compat1.3 revert to BLAST version 1.3 behavior (with bug fixes) -dbtop search only the top strand of the database -dbbottom search only the bottom strand of the database -dbgcode # specify a genetic code for the database -filter method (e.g., methods of "seg", "xnu", or "seg+xnu") -echofilter display the filtered query sequence -hitdist # max. distance between word hits for 2-hit BLAST (default 0) -wink # generate neighborhood words every wink-th position (default 1) -stats collect word-hit statistics (consumes a little additional cpu time) -ctxfactor # base statistics on this number of independent contexts or reading frames -nogap turn off gapped alignment method, report only ungapped HSPs -gapE # expectation threshold of ungapped HSP sets for seeding gapped alignments -gapall perform gapped alignment procedure on all ungapped HSPs (slower) -gapE2 # expectation threshold for saving individual gapped alignments (GSPs) -gapS2 # cutoff score for saving individual gapped alignments -gapW # band width (full, not half) for gapped alignment procedure -postsw perform full Smith-Waterman before output (BLASTP only) -olf # max. fractional length of overlap for HSP consistency -golf # max. fractional length overlap for GSP consistency -gapdecayrate # -span2 discard HSPs spanned on both query and subject by a better HSP* -span1 discard HSPs spanned on query, subject or both by a better HSP -span do not discard HSPs spanned by other, better HSPs -prune do not prune insignificant HSPs from the output lists -edegrade # only show HSP combos within this factor of the best combo -consistency turn off HSP consistency rules for statistics -nonnegok make all non-negative expected scores a non-FATAL error -novalidctxok make no valid contexts a non-FATAL error -hspsepqmax max. separation allowed between HSPs along query -hspsepsmax max. separation allowed between HSPs along subject -gapsepqmax max. separation allowed between GSPs along query -gapsepsmax max. separation allowed between GSPs along subject -matrix matrixfile specify a scoring matrix file -altscore qc,sc,score qc and sc may be letters or "all"; score may be #, "min", "max", or "na" -hspmax # max. no. of HSPs saved/reported per subject sequence, default 1000 -qoffset # adjust query coordinate numbering by this amount -dbrecmin # starting database record number to search -dbrecmax # ending database record number to search -gi display gi identifiers, when available -noseqs do not display sequence alignments -- abbreviated output -qtype exit non-zero if query seems to be of wrong type -qres exit non-zero if query contains an invalid residue code -sort_by_pvalue -sort_by_count -sort_by_highscore -sort_by_totalscore -cpus # no. of processors to utilize on multi-processor systems -mmio do not use memory-mapped I/O (usually slower) -notes suppress informatory messages -warnings suppress warning messages -errors suppress non-fatal error messages -abortonerror abort (and possibly dump core) on a non-fatal error -abortonfatal abort (and possibly dump core) on a fatal error -progress # report progress of search at least this often (seconds) -o fname write output to file named "fname", instead of stdout -asn1 produce ASN.1 "print-value" output (currently broken) -asn1bin produce binary-encoded ASN.1 output (currently broken) *Default program behavior
TBLASTX 2.0MP-WashU [09-Sep-1999] [irix6-r10k-b64 12:19:05 09-Sep-1999] Copyright (C) 1996-1999 Washington University, Saint Louis, Missouri USA. All Rights Reserved. Reference: Gish, W. (1996-1999) http://blast.wustl.edu Notice: statistical significance is estimated under the assumption that the equivalent of one entire reading frame of the query sequence and one entire reading frame of the database code for protein and that significant alignments will only involve coding reading frames. Usage: TBLASTX database queryfile [options] Valid TBLASTX options: E, S, E2, S2, W, T, X, M, C, Y, Z, H, V and B -sump use Karlin-Altschul "Sum" statistics* -poissonp use Poisson statistics to evaluate multiple HSPs -compat1.4 revert to BLAST version 1.4 behavior (with bug fixes) -compat1.3 revert to BLAST version 1.3 behavior (with bug fixes) -top search only the top strand of the query -bottom search only the bottom strand of the query -dbtop search only the top strand of the database -dbbottom search only the bottom strand of the database -dbgcode # specify a genetic code for the database -filter method (e.g., methods of "seg", "xnu", or "seg+xnu") -echofilter display the filtered query sequence -hitdist # max. distance between word hits for 2-hit BLAST (default 0) -wink # generate neighborhood words every wink-th position (default 1) -stats collect word-hit statistics (consumes a little additional cpu time) -ctxfactor # base statistics on this number of independent contexts or reading frames -nogap turn off gapped alignment method, report only ungapped HSPs -gapE # expectation threshold of ungapped HSP sets for seeding gapped alignments -gapall perform gapped alignment procedure on all ungapped HSPs (slower) -gapE2 # expectation threshold for saving individual gapped alignments (GSPs) -gapS2 # cutoff score for saving individual gapped alignments -gapW # band width (full, not half) for gapped alignment procedure -postsw perform full Smith-Waterman before output (BLASTP only) -olf # max. fractional length of overlap for HSP consistency -golf # max. fractional length overlap for GSP consistency -gapdecayrate # -span2 discard HSPs spanned on both query and subject by a better HSP* -span1 discard HSPs spanned on query, subject or both by a better HSP -span do not discard HSPs spanned by other, better HSPs -prune do not prune insignificant HSPs from the output lists -edegrade # only show HSP combos within this factor of the best combo -consistency turn off HSP consistency rules for statistics -nonnegok make all non-negative expected scores a non-FATAL error -novalidctxok make no valid contexts a non-FATAL error -hspsepqmax max. separation allowed between HSPs along query -hspsepsmax max. separation allowed between HSPs along subject -gapsepqmax max. separation allowed between GSPs along query -gapsepsmax max. separation allowed between GSPs along subject -matrix matrixfile specify a scoring matrix file -altscore qc,sc,score qc and sc may be letters or "all"; score may be #, "min", "max", or "na" -hspmax # max. no. of HSPs saved/reported per subject sequence, default 1000 -qoffset # adjust query coordinate numbering by this amount -dbrecmin # starting database record number to search -dbrecmax # ending database record number to search -gi display gi identifiers, when available -noseqs do not display sequence alignments -- abbreviated output -qtype exit non-zero if query seems to be of wrong type -qres exit non-zero if query contains an invalid residue code -sort_by_pvalue -sort_by_count -sort_by_highscore -sort_by_totalscore -cpus # no. of processors to utilize on multi-processor systems -mmio do not use memory-mapped I/O (usually slower) -notes suppress informatory messages -warnings suppress warning messages -errors suppress non-fatal error messages -abortonerror abort (and possibly dump core) on a non-fatal error -abortonfatal abort (and possibly dump core) on a fatal error -progress # report progress of search at least this often (seconds) -o fname write output to file named "fname", instead of stdout -asn1 produce ASN.1 "print-value" output (currently broken) -asn1bin produce binary-encoded ASN.1 output (currently broken) *Default program behavior
Goback 
Bork Group 
EMBL