| /dports/biology/py-biopython/biopython-1.79/Doc/Tutorial/ |
| H A D | chapter_blast.tex | 1 \chapter{BLAST} chapter
24 for dealing with NCBI BLAST.
158 \section{Running BLAST locally}
166 \item Local BLAST may be faster than BLAST over the internet;
188 {NCBI BLAST+} suite was released in 2009. This replaces the old NCBI ``legacy'' BLAST
257 BLAST} (AB-BLAST, released in 2009, not free/open source). These packages include
263 \section{Parsing BLAST output}
344 get BLAST record objects.
349 the BLAST output, retrieving BLAST records one by one for each BLAST
400 \section{The BLAST record class}
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| /dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Index/ |
| H A D | BlastTable.pm | 193 open my $BLAST, '<', $file or $self->throw("Could not read file '$file': $!");
203 my $init_pos = tell($BLAST);
204 my $curr_line = <$BLAST>;
205 my $pos_diff = tell($BLAST) - $init_pos;
207 seek $BLAST, $init_pos, 0; # Rewind position to proceed to read the file
209 while( <$BLAST> ) {
213 $indexpoint = tell($BLAST) - length($_) - $correction;
220 $indexpoint = tell($BLAST) - length($_) - $correction unless $is_m9;
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| H A D | Blast.pm | 215 open my $BLAST, '<', $file or $self->throw("Could not read file '$file': $!");
226 my $init_pos = tell($BLAST);
227 my $curr_line = <$BLAST>;
228 my $pos_diff = tell($BLAST) - $init_pos;
230 seek $BLAST, $init_pos, 0; # Rewind position to proceed to read the file
233 while( my $line = <$BLAST> ) {
241 $indexpoint = tell($BLAST) - length($line) - $correction;
245 $indexpoint = tell($BLAST) - length($line) - $correction if ( $prefix eq 'RPS-' );
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| /dports/biology/ncbi-toolkit/ncbi/network/wwwblast/ |
| H A D | README.rps | 4 RPS-BLAST (Reverse PSI-BLAST) searches a query sequence against a database
5 of profiles. This is the opposite of PSI-BLAST that searches a profile
6 against a database of sequences, hence the 'Reverse'. RPS-BLAST
7 uses a BLAST-like algorithm, finding single- or double-word hits
16 RPS-BLAST uses a BLAST database, with addition of some other files that
25 The CD-Search databases for RPS-BLAST can be found at:
44 of PSI-BLAST, into portable ASCII form);
50 formatdb : general BLAST database formatter.
53 matrices, prepared by copymat, producing BLAST-like output).
64 i. a collection of PSI-BLAST-generated profiles with arbitrary
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| /dports/biology/ncbi-toolkit/ncbi/asn/ |
| H A D | scoremat.asn | 107 -- PSI-BLAST, formatrpsdb, RPS-BLAST workflow:
110 -- Two possible inputs to PSI-BLAST and formatrpsdb:
117 -- the PSI-BLAST search or build the PSSM to then build the RPS-BLAST database.
121 -- build the PSSM and ultimately the RPS-BLAST database
125 -- PssmWithParams ====> + PSI-BLAST + =====> PssmWithParams
136 -- | formatrpsdb | =====> | RPS-BLAST databases | |
142 -- | RPS-BLAST | |
176 -- RPS-BLAST database are scaled by the same factor (otherwise, RPS-BLAST
315 -- are the PSI-BLAST options specified using the BLAST options API
323 -- populated by PSI-BLAST
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/scoremat/ |
| H A D | scoremat.asn | 107 -- PSI-BLAST, formatrpsdb, RPS-BLAST workflow:
110 -- Two possible inputs to PSI-BLAST and formatrpsdb:
117 -- the PSI-BLAST search or build the PSSM to then build the RPS-BLAST database.
121 -- build the PSSM and ultimately the RPS-BLAST database
125 -- PssmWithParams ====> + PSI-BLAST + =====> PssmWithParams
136 -- | formatrpsdb | =====> | RPS-BLAST databases | |
142 -- | RPS-BLAST | |
176 -- RPS-BLAST database are scaled by the same factor (otherwise, RPS-BLAST
318 -- are the PSI-BLAST options specified using the BLAST options API
326 -- populated by PSI-BLAST
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/scoremat/ |
| H A D | scoremat.asn | 107 -- PSI-BLAST, formatrpsdb, RPS-BLAST workflow:
110 -- Two possible inputs to PSI-BLAST and formatrpsdb:
117 -- the PSI-BLAST search or build the PSSM to then build the RPS-BLAST database.
121 -- build the PSSM and ultimately the RPS-BLAST database
125 -- PssmWithParams ====> + PSI-BLAST + =====> PssmWithParams
136 -- | formatrpsdb | =====> | RPS-BLAST databases | |
142 -- | RPS-BLAST | |
176 -- RPS-BLAST database are scaled by the same factor (otherwise, RPS-BLAST
318 -- are the PSI-BLAST options specified using the BLAST options API
326 -- populated by PSI-BLAST
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| /dports/biology/ugene/ugene-40.1/data/workflow_samples/Scenarios/ |
| H A D | remote_blasting.uwl | 2 …eral sequences as input. For each sequence it sends a request to the NCBI BLAST remote database to…
3 #The following options are set to the BLAST search by default:
4 # 1) Nucleotide BLAST database is used.
5 …for high similar sequences (i.e. the "Megablast" option is selected) as on the NCBI BLAST web site.
7 #As the result of the BLAST each input sequence is annotated with the "blast result" annotations.
9 #The output homologous sequences and the original sequences, annotated by BLAST, are grouped by fol…
22 name:"Write Original Sequence(s) with BLAST Annotations";
36 name:"Remote BLAST";
41 name:"Fetch Sequences by ID from BLAST Annotations";
141 title:"Remote Nucleotide BLAST";
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| /dports/net-mgmt/mrtg/mrtg-2.17.4/contrib/mrtg-blast/ |
| H A D | mrtg-blast | 56 unless (open(BLAST, "/home/netadmin/mrtg-2.1/tcpblast -r -t $host $packets -p$port|")) {
61 while (<BLAST>) {
64 …close(BLAST), return("$4.$5") if /^(\d+) KB in (\d+) msec = (\d+)\.\d b\/s = (\d+)\.\d B\/s =…
68 close(BLAST), return(0);
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| /dports/biology/ugene/ugene-40.1/data/cmdline/ |
| H A D | local-blast+.uwl | 2 #Run local NCBI BLAST search. BLAST finds regions of similarity between biological sequences. Must …
22 name:"Local BLAST+ search";
52 description:"Location of BLAST output file";
56 description:"Type of BLAST searches (using 'blastn' by default)";
60 description:"Base name for BLAST DB files";
88 description:"BLAST+ location (using the path specified in UGENE by default)";
92 description:"Type of BLAST output file (using 'XML (-outfmt 5)' by default)";
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| H A D | gene-by-gene.uwl | 4 #1. Create a local BLAST+ db of your genome sequence/contigs. One db per one genome.
6 #3. Setup location and name of BLAST+ db you created for the first genome.
7 #4. Setup output files: report location and output file with annotated (with BLAST+) sequence. You …
9 #5*. Run the scheme on the same input and output files changing BLAST+ db for each genome that you …
30 name:"Local BLAST+ Search";
60 …"Identity between gene sequence length and annotation length in per cent. BLAST+ identity (if spec…
68 description:"Location of BLAST+ output file";
72 description:"Type of BLAST+ searches (using 'blastn' by default)";
80 description:"Name of BLAST+ DB";
84 description:"Path of BLAST+ DB";
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| /dports/biology/ncbi-toolkit/ncbi/tools/ |
| H A D | blstxml.asn | 7 program VisibleString , -- BLAST program: blastp, tblastx etc.
10 db VisibleString , -- BLAST Database name
17 mbstat Statistics OPTIONAL -- Mega BLAST search statistics
37 pattern VisibleString OPTIONAL, -- PHI-BLAST pattern
42 db-num INTEGER , -- Number of sequences in BLAST db
43 db-len BigInt , -- Length of BLAST db
69 pattern-from INTEGER OPTIONAL , -- start of PHI-BLAST pattern
70 pattern-to INTEGER OPTIONAL , -- end of PHI-BLAST pattern
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/blastxml/ |
| H A D | blastxml.asn | 7 program VisibleString , -- BLAST program: blastp, tblastx etc.
10 db VisibleString , -- BLAST Database name
17 mbstat Statistics OPTIONAL -- Mega BLAST search statistics
37 pattern VisibleString OPTIONAL, -- PHI-BLAST pattern
42 db-num INTEGER , -- Number of sequences in BLAST db
43 db-len BigInt , -- Length of BLAST db
69 pattern-from INTEGER OPTIONAL , -- start of PHI-BLAST pattern
70 pattern-to INTEGER OPTIONAL , -- end of PHI-BLAST pattern
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/blastxml/ |
| H A D | blastxml.asn | 7 program VisibleString , -- BLAST program: blastp, tblastx etc.
10 db VisibleString , -- BLAST Database name
17 mbstat Statistics OPTIONAL -- Mega BLAST search statistics
37 pattern VisibleString OPTIONAL, -- PHI-BLAST pattern
42 db-num INTEGER , -- Number of sequences in BLAST db
43 db-len BigInt , -- Length of BLAST db
69 pattern-from INTEGER OPTIONAL , -- start of PHI-BLAST pattern
70 pattern-to INTEGER OPTIONAL , -- end of PHI-BLAST pattern
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| /dports/biology/ncbi-toolkit/ncbi/network/wwwblast/Src/XML/ |
| H A D | blstxml.asn | 6 -- ASN.1 for simplified BLAST output in XML
44 program VisibleString , -- BLAST program: blastp, tblastx etc.
47 db VisibleString , -- BLAST Database name
54 mbstat Statistics OPTIONAL -- Mega BLAST search statistics
74 pattern VisibleString OPTIONAL, -- PHI-BLAST pattern
79 db-num INTEGER , -- Number of sequences in BLAST db
80 db-len INTEGER , -- Length of BLAST db
106 pattern-from INTEGER OPTIONAL , -- start of PHI-BLAST pattern
107 pattern-to INTEGER OPTIONAL , -- end of PHI-BLAST pattern
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/scripts/projects/magicblast/post_build/rpm/ |
| H A D | ncbi-magicblast.spec | 5 Summary: NCBI Magic-BLAST is a tool for mapping next-generation RNA or DNA sequencing runs agai…
7 Group: NCBI/BLAST
16 NCBI Magic-BLAST is a specialized variant of BLAST designed for mapping
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/scripts/projects/magicblast/post_build/rpm/ |
| H A D | ncbi-magicblast.spec | 5 Summary: NCBI Magic-BLAST is a tool for mapping next-generation RNA or DNA sequencing runs agai…
7 Group: NCBI/BLAST
16 NCBI Magic-BLAST is a specialized variant of BLAST designed for mapping
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/scripts/projects/quickblastp/post_build/rpm/ |
| H A D | ncbi-magicblast.spec | 5 Summary: NCBI Magic-BLAST is a tool for mapping next-generation RNA or DNA sequencing runs agai…
7 Group: NCBI/BLAST
16 NCBI Magic-BLAST is a specialized variant of BLAST designed for mapping
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/scripts/projects/quickblastp/post_build/rpm/ |
| H A D | ncbi-magicblast.spec | 5 Summary: NCBI Magic-BLAST is a tool for mapping next-generation RNA or DNA sequencing runs agai…
7 Group: NCBI/BLAST
16 NCBI Magic-BLAST is a specialized variant of BLAST designed for mapping
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| /dports/biology/hmmer/hmmer-3.3/easel/demotic/ |
| H A D | test.pl | 7 open(BLAST, "blastp $swiss_wu example.fa 2>/dev/null |");
8 while (demotic_blast::parse(\*BLAST))
14 close BLAST;
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| /dports/biology/infernal/infernal-1.1.3/easel/demotic/ |
| H A D | test.pl | 7 open(BLAST, "blastp $swiss_wu example.fa 2>/dev/null |");
8 while (demotic_blast::parse(\*BLAST))
14 close BLAST;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/read_blast_result/ |
| H A D | README.standalone | 32 pre-computed using BLAST and its modifications and tRNAscanSE. Currently
69 input file which contains the standard BLAST output results (ran with -IT
74 input file which contains the standard BLAST output results for all query
84 excluded from BLAST output results
105 the same subject (common BLAST hit) by comparing BLAST results. Since gene
106 fusions/splits occur in prokaryotic genes the BLAST hits are analyzed for any
107 subject (not the common BLAST hit) that covers 90% of the query protein, in
111 partial - The results from the RPS-BLAST against conserved domains are analyzed
154 BLAST - either standalone or web-based tool, both available at NCBI - to run
158 for creating BLAST databases can be found in the BLAST documents. BLAST output
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
| H A D | README | 1 This directory contains the implementation of the core of the BLAST algorithm
2 (also known as the BLAST engine). In the future, NCBI may provide a simple
8 such as BLAST database access, BLAST formatting, embedded logging, MT locking,
13 Download the source distribution of BLAST+:
22 To build these source files into a library without the rest of the NCBI BLAST+
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
| H A D | README | 1 This directory contains the implementation of the core of the BLAST algorithm
2 (also known as the BLAST engine). In the future, NCBI may provide a simple
8 such as BLAST database access, BLAST formatting, embedded logging, MT locking,
13 Download the source distribution of BLAST+:
22 To build these source files into a library without the rest of the NCBI BLAST+
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/dbindex/ |
| H A D | README.usage | 2 DATABASE INDEXING IMPLEMENTATION FOR NUCLEOTIDE SEARCH IN NCBI BLAST
45 NOTE: Some of the functionality has changed in BLAST verison 2.2.27.
55 take either a fasta formatted file or an existing BLAST database as
66 fasta formatted file or a BLAST database. The type is selected by
67 'iformat' option and is fasta by default. BLAST databases are
68 searched using the same rules as used by other NCBI BLAST applications.
84 New style indices are considered part of the BLAST database and
108 BLAST databases. Indices do not replace BLAST databases completely:
130 different from the name of the BLAST database. This option can
137 corresponding the BLAST database.
|