1# tempdata - this is the directory used by the test databases TEMBL, TSW, etc. 2# If you use these databases for testing you must uncomment this line and set 3# the definition to the directory where the databases are installed. 4# By default this is /usr/local/share/EMBOSS/test but the directory can 5# be changed with --prefix when you configure EMBOSS. 6 7# SET emboss_tempdata %%DATADIR%%/test 8 9# Proxy - set this if any databases are accessed through a proxy web server. 10# Turn off in the DB definition with proxy: ":" for any 11# databases that are internal and should not go through the proxy. 12 13# SET emboss_proxy "proxy.mydomain.ac.uk:8080" 14 15# Logfile - set this to a file that any user can append to 16# and EMBOSS applications will automatically write log information 17 18# SET emboss_logfile /var/log/emboss.log 19 20# Pagesize - this is the size of disc page blocks and is 21# required by the 'dbx' indexing programs and 'method: emboss' 22# We recommend a value of 2048 23 24SET PAGESIZE 2048 25 26# Cachesize - a cache of disc pages to be used by the 'dbx' 27# indexing system and is required for 'method emboss'. It is 28# the number of PAGESIZE blocks to cache. We recommend 29# a value of 200 30 31SET CACHESIZE 200 32 33################################################################## 34# Test Databases 35# Used by the qatest.pl script to test an EMBOSS installation. 36# Comment them out if you do not want your users to use them. 37# Examples in the EMBOSS documentation should all run by using 38# TEMBL: in place of EMBL:, TSW: in place of SW:, and so on. 39################################################################## 40 41 42# swissprot (Puffer fish entries) 43# ========= 44 45DB tsw [ type: P dir: $emboss_tempdata/swiss 46 method: emblcd format: swiss release: 36 47 fields: "sv des org key" 48 comment: "Swissprot native format with EMBL CD-ROM index" ] 49 50# swnew (Puffer fish entries) 51# ===== 52 53DB tswnew [ type: P dir: $emboss_tempdata/swnew 54 method: emblcd format: swiss release: 37 55 fields: "sv des org key" 56 comment: "Swissnew as 3 files in native format with EMBL CD-ROM index" ] 57 58# wormpep (cosmid ZK637) 59# ======= 60 61DB twp [ type: P dir: $emboss_tempdata/wormpep 62 method: emblcd format: fasta release: 16 63 fields: "des" 64 comment: "EMBL new in native format with EMBL CD-ROM index" ] 65 66# embl (worm cosmid ZK637 and a few other entries) 67# ==== 68 69DB tembl [ type: N dir: $emboss_tempdata/embl 70 method: emblcd format: embl release: 57 71 fields: "sv des org key" 72 comment: "EMBL in native format with EMBL CD-ROM index" ] 73 74# pir (cytochrome C plus first entries in other divisions) 75# === 76 77DB tpir [ type: P dir: $emboss_tempdata/pir 78 method: gcg 79 file: pir*.seq 80 format: nbrf 81 fields: "des org key" 82 comment: "PIR using NBRF access for 4 files" ] 83 84# Genbank (Canadian EMBnet node - so long as they are running SRS version 6) 85# ======= 86 87DB tgb [ type: N method: srswww format: genbank 88 url: "http://cbr-rbc.nrc-cnrc.gc.ca/srs6bin/cgi-bin/wgetz" 89 dbalias: genbankrelease 90 fields: "sv des org key" 91 comment: "Genbank IDs" ] 92 93# Genbank (local copy of the TEMBL entries from Genbank) 94# ======= 95 96DB tgenbank [ type: N dir: $emboss_tempdata/genbank 97 method: emblcd format: genbank release: 01 98 fields: "sv des org key" 99 comment: "GenBank in native format with EMBL CD-ROM index" ] 100 101############################################# 102# DATABASE SETTING EXAMPLES 103# 104# Modify these for your own 105# local and remote database definitions 106# 107# See the EMBOSS Administrators Guide 3.0.0 108# for full documentation on DB definitions. 109############################################# 110 111####################################################################### 112# GENBANK from the Canadian EMBnet node SRSWWW server 113####################################################################### 114 115 116#DB genbank [ type: N method: url format: genbank 117# url: "http://www.ca.embnet.org/srs6bin/cgi-bin/wgetz?-id+-e+[genbank-id:'%s']+-vn+2" 118# comment: "Genbank IDs" ] 119 120#DB gb [ type: N method: url format: genbank 121# url: "http://www.ca.embnet.org/srs6bin/cgi-bin/wgetz?-id+-e+[genbank-id:'%s']+-vn+2" 122# comment: "Genbank IDs" ] 123 124#DB genbanka [ type: N method: url format: genbank 125# url: "http://www.ca.embnet.org/srs6bin/cgi-bin/wgetz?-id+-e+[genbank-acc:'%s']+-vn+2" 126# comment: "Genbank ACs" ] 127 128#DB gba [ type: N method: url format: genbank 129# url: "http://www.ca.embnet.org/srs6bin/cgi-bin/wgetz?-id+-e+[genbank-acc:'%s']+-vn+2" 130# comment: "Genbank ACs" ] 131 132## N.B. 133# For older SRS servers use e.g. 134#DB gb [ type: N method: url format: genbank 135# url: "http://srs.csc.fi:8002/srs6bin/cgi-bin/wgetz?-e+[genbank-id:%s]" 136# comment: "Genbank IDs" ] 137 138 139 140 141####################################################################### 142# PIR/NBRF indexed with dbigcg 143####################################################################### 144 145# Set the directory to where the database is stored 146# Assumed the dbigcg index files are in the same directory 147 148# DB pir [ type: P dir: /data/pir 149# method: gcg 150# file: pir*.seq 151# format: nbrf 152# comment: "PIR/NBRF" ] 153 154# DB nbrf [ type: P dir: /data/pir 155# method: gcg 156# file: pir*.seq 157# format: nbrf 158# comment: "PIR/NBRF" ] 159 160 161 162 163########################################################################## 164# SWISSPROT indexed with dbiflat 165########################################################################## 166 167# SWISSPROT: Set the directory to where the database is stored 168# Assumed the dbiflat index files are in the same directory 169 170# DB swissprot [ 171# type: P 172# comment: "SWISSPROT sequences" 173# method: emblcd 174# format: swiss 175# dbalias: swissprot 176# dir: /data/swissprot/ 177# file: seq.dat 178# ] 179 180# SWISSNEW: Set the directory to where the database is stored 181# Assumed the dbiflat index files are in the same directory 182 183# DB sw [ 184# type: P 185# comment: "SWISSPROT sequences" 186# method: emblcd 187# format: swiss 188# dbalias: swissprot 189# dir: /data/swissprot/ 190# file: seq.dat 191# ] 192 193 194 195######################################################### 196# EMBL indexed with dbiflat 197######################################################### 198 199# EMBL: Set the directory to where the database is stored 200# Assumed the dbiflat index files are in the same directory 201# Second definition is another name for the first. 202 203#DB embl [ type: N method: emblcd release: "61.0" 204# format: embl dir: /data/embl/ 205# file: *.dat comment: "EMBL sequences" 206#] 207 208#DB em [ type: N method: emblcd release: "61.0" 209# format: embl dir: /data/embl/ 210# file: *.dat comment: "EMBL sequences" 211#] 212 213 214## Old EMBL definitions (for historical reasons) using SRSWWW 215##DB embla [ type: N method: url format: embl 216## url: "http://srs.hgmp.mrc.ac.uk/srs6bin/cgi-bin/wgetz?-e+[embl-acc:%s]" 217## comment: "Use embl instead!" ] 218## 219##DB ema [ type: N method: url format: embl 220## url: "http://srs.hgmp.mrc.ac.uk/srs6bin/cgi-bin/wgetz?-e+[embl-acc:%s]" 221## comment: "Use embl instead!" ] 222 223######################################################### 224# EMBL NEW 225######################################################### 226 227# EMBLNEW: Set the directory to where the database is stored 228# Assumed the dbiflat index files are in the same directory 229 230# DB emblnew [ type: N method: emblcd release: "0.0" 231# format: embl dir: /data/embl/newdata/ 232# file: *.dat comment: "New EMBL sequences" 233# ] 234 235 236 237########################################################## 238# EMBL subdivisions using the original EMBL dbiflat indices 239########################################################## 240 241# Simply redefine EMBL with exclude: and file: to limit 242# the database files available 243 244# DB fungal [ type: N method: emblcd release: "61.0" 245# format: embl dir: /data/embl/ exclude: *.dat 246# file: */fun*.dat comment: "EMBL fungal sequences" 247# ] 248 249# DB est [ type: N method: emblcd release: "61.0" 250# format: embl dir: /data/embl/ exclude: *.dat 251# file: */est*.dat comment: "EMBL EST sequences" 252# ] 253 254# DB gss [ type: N method: emblcd release: "61.0" 255# format: embl dir: /data/embl/ exclude: *.dat 256# file: */gss*.dat comment: "EMBL GSS sequences" 257# ] 258 259# DB htg [ type: N method: emblcd release: "61.0" 260# format: embl dir: /data/embl/ exclude: *.dat 261# file: */htg*.dat comment: "EMBL HTG sequences" 262# ] 263 264# DB human [ type: N method: emblcd release: "61.0" 265# format: embl dir: /data/embl/ exclude: *.dat 266# file: */hum?.dat comment: "EMBL human sequences" 267# ] 268 269# DB humanest [ type: N method: emblcd release: "61.0" 270# format: embl dir: /data/embl/est/ exclude: *.dat 271# file: */humanest*.dat comment: "EMBL human EST sequences" 272# ] 273 274# DB invertebrate [ type: N method: emblcd release: "61.0" 275# format: embl dir: /data/embl/ exclude: *.dat 276# file: */inv*.dat comment: "EMBL invertebrate sequences" 277# ] 278 279# DB mammalian [ type: N method: emblcd release: "61.0" 280# format: embl dir: /data/embl/ exclude: *.dat 281# file: */mam*.dat comment: "EMBL mammalian sequences" 282# ] 283 284# DB mouseest [ type: N method: emblcd release: "61.0" 285# format: embl dir: /data/embl/est/ exclude: *.dat 286# file: */mouseest*.dat comment: "EMBL mouse EST sequences" 287# ] 288 289# DB organelle [ type: N method: emblcd release: "61.0" 290# format: embl dir: /data/embl/ exclude: *.dat 291# file: */org*.dat comment: "EMBL organelle sequences" 292# ] 293 294# DB otherest [ type: N method: emblcd release: "61.0" 295# format: embl dir: /data/embl/est/ exclude: *.dat 296# file: */otherest*.dat comment: "EMBL other EST sequences" 297# ] 298 299# DB patent [ type: N method: emblcd release: "61.0" 300# format: embl dir: /data/embl/ exclude: *.dat 301# file: */patent*.dat comment: "EMBL patented sequences" 302# ] 303 304# DB phage [ type: N method: emblcd release: "61.0" 305# format: embl dir: /data/embl/ exclude: *.dat 306# file: */phg*.dat comment: "EMBL phage sequences" 307# ] 308 309# DB plant [ type: N method: emblcd release: "61.0" 310# format: embl dir: /data/embl/ exclude: *.dat 311# file: */pln*.dat comment: "EMBL plant sequences" 312# ] 313 314# DB prokaryotic [ type: N method: emblcd release: "61.0" 315# format: embl dir: /data/embl/ exclude: *.dat 316# file: */pro*.dat comment: "EMBL prokaryotic sequences" 317# ] 318 319# DB rodent [ type: N method: emblcd release: "61.0" 320# format: embl dir: /data/embl/ exclude: *.dat 321# file: */rod*.dat comment: "EMBL rodent sequences" 322# ] 323 324# DB sts [ type: N method: emblcd release: "61.0" 325# format: embl dir: /data/embl/ exclude: *.dat 326# file: */sts*.dat comment: "EMBL STS sequences" 327# ] 328 329# DB synthetic [ type: N method: emblcd release: "61.0" 330# format: embl dir: /data/embl/ exclude: *.dat 331# file: */syn*.dat comment: "EMBL synthetic sequences" 332# ] 333 334# DB unclassified [ type: N method: emblcd release: "61.0" 335# format: embl dir: /data/embl/ exclude: *.dat 336# file: */unc*.dat comment: "EMBL unclassified sequences" 337# ] 338 339# DB viral [ type: N method: emblcd release: "61.0" 340# format: embl dir: /data/embl/ exclude: *.dat 341# file: */vrl*.dat comment: "EMBL viral sequences" 342# ] 343 344# DB othervertebrate [ type: N method: emblcd release: "61.0" 345# format: embl dir: /data/embl/ exclude: *.dat 346# file: */vrt*.dat comment: "EMBL other vertebrate sequences" 347# ] 348 349# DB vertebrate [ type: N method: emblcd release: "61.0" 350# format: embl dir: /data/embl/ exclude: *.dat 351# file: "*/vrt*.dat */mam*.dat */rod*.dat" 352# comment: "EMBL vertebrate sequences" 353# ] 354 355 356#################################################################### 357# TREMBL databases indexed with dbiflat 358#################################################################### 359 360# TREMBL: Set the directory to where the database is stored 361# Assumed the dbiflat index files are in the same directory 362 363# DB trembl [ 364# type: P 365# comment: "TREMBL sequences" 366# method: emblcd 367# format: swiss 368# dir: /data/trembl/ 369# file: tr_*.dat 370# ] 371 372# SPTREMBL: Set the directory to where the database is stored 373# Assumed the dbiflat index files are in the same directory 374 375# DB sptrembl [ 376# type: P 377# comment: "SPTREMBL sequences" 378# method: emblcd 379# format: swiss 380# dir: /data/trembl/sptrembl/ 381# file: tr_*.dat 382# ] 383 384# DB remtrembl [ 385# type: P 386# comment: "REMTREMBL sequences" 387# method: emblcd 388# format: swiss 389# dir: /data/trembl/sptrembl/ 390# file: tr_*.dat 391# ] 392 393 394 395#################################################################### 396# New TREMBL 397#################################################################### 398 399# TREMBLNEW: Set the directory to where the database is stored 400# Assumed the dbiflat index files are in the same directory 401 402# DB tremblnew [ 403# type: P 404# comment: "New TREMBL sequences" 405# method: emblcd 406# format: swiss 407# dir: /data/trembl/emboss/ 408# file: tremblnew*.dat 409# ] 410 411 412 413#################################################################### 414# Trembl subsections 415#################################################################### 416 417# Simply redefine TREMBL with exclude: and file: to limit 418# the database files available 419 420# DB trarc [ type: P method: emblcd release: "61.0" 421# format: swiss dir: /data/trembl/ exclude: *.dat 422# file: */tr_arc*.dat comment: "TREMBL ARC sequences" 423# ] 424 425# DB trfungal [ type: P method: emblcd release: "61.0" 426# format: swiss dir: /data/trembl/ exclude: *.dat 427# file: */tr_fun*.dat comment: "TREMBL fungal sequences" 428# ] 429 430# DB trhuman [ type: P method: emblcd release: "61.0" 431# format: swiss dir: /data/trembl/ exclude: *.dat 432# file: */tr_hum*.dat comment: "TREMBL human sequences" 433# ] 434 435# DB trimmuno [ type: P method: emblcd release: "61.0" 436# format: swiss dir: /data/trembl/ exclude: *.dat 437# file: */tr_immuno*.dat comment: "TREMBL immunological sequences" 438# ] 439 440# DB trinvertebrate [ type: P method: emblcd release: "61.0" 441# format: swiss dir: /data/trembl/ exclude: *.dat 442# file: */tr_inv*.dat comment: "TREMBL invertebrate sequences" 443# ] 444 445# DB trmammalian [ type: P method: emblcd release: "61.0" 446# format: swiss dir: /data/trembl/ exclude: *.dat 447# file: */tr_mam*.dat comment: "TREMBL mammalian sequences" 448# ] 449 450# DB trmhc [ type: P method: emblcd release: "61.0" 451# format: swiss dir: /data/trembl/ exclude: *.dat 452# file: */tr_mhc*.dat comment: "TREMBL MHC sequences" 453# ] 454 455# DB trorganelle [ type: P method: emblcd release: "61.0" 456# format: swiss dir: /data/trembl/ exclude: *.dat 457# file: */tr_org*.dat comment: "TREMBL organelle sequences" 458# ] 459 460# DB trpatent [ type: P method: emblcd release: "61.0" 461# format: swiss dir: /data/trembl/ exclude: *.dat 462# file: */tr_patent*.dat comment: "TREMBL patented sequences" 463# ] 464 465# DB trphage [ type: P method: emblcd release: "61.0" 466# format: swiss dir: /data/trembl/ exclude: *.dat 467# file: */tr_phg*.dat comment: "TREMBL phage sequences" 468# ] 469 470# DB trplant [ type: P method: emblcd release: "61.0" 471# format: swiss dir: /data/trembl/ exclude: *.dat 472# file: */tr_pln*.dat comment: "TREMBL plant sequences" 473# ] 474 475# DB trprokaryotic [ type: P method: emblcd release: "61.0" 476# format: swiss dir: /data/embl/ exclude: *.dat 477# file: */tr_pro*.dat comment: "TREMBL prokaryotic sequences" 478# ] 479 480# DB trpseudo [ type: P method: emblcd release: "61.0" 481# format: embl dir: /data/trembl/ exclude: *.dat 482# file: */tr_pseudo*.dat comment: "TREMBL pseudo sequences" 483# ] 484 485# DB trrodent [ type: P method: emblcd release: "61.0" 486# format: swiss dir: /data/trembl/ exclude: *.dat 487# file: */tr_rod*.dat comment: "TREMBL rodent sequences" 488# ] 489 490# DB trsmall [ type: P method: emblcd release: "61.0" 491# format: swiss dir: /data/trembl/ exclude: *.dat 492# file: */tr_smalls*.dat comment: "TREMBL small sequences" 493# ] 494 495# DB trsynthetic [ type: P method: emblcd release: "61.0" 496# format: swiss dir: /data/trembl/ exclude: *.dat 497# file: */tr_syn*.dat comment: "TREMBL synthetic sequences" 498# ] 499 500# DB trtruncated [ type: P method: emblcd release: "61.0" 501# format: swiss dir: /data/trembl/ exclude: *.dat 502# file: */tr_truncated*.dat comment: "TREMBL truncated sequences" 503# ] 504 505# DB trunclassified [ type: P method: emblcd release: "61.0" 506# format: swiss dir: /data/trembl/ exclude: *.dat 507# file: */tr_unc*.dat comment: "TREMBL unclassified sequences" 508# ] 509 510# DB trviral [ type: P method: emblcd release: "61.0" 511# format: swiss dir: /data/trembl/ exclude: *.dat 512# file: */tr_vrl*.dat comment: "TREMBL viral sequences" 513# ] 514 515# DB trothervertebrate [ type: P method: emblcd release: "61.0" 516# format: swiss dir: /data/trembl/ exclude: *.dat 517# file: */tr_vrt*.dat comment: "TREMBL other vertebrate sequences" 518# ] 519 520 521 522#################################################################### 523# Biomart example 524#################################################################### 525 526#DB martensembl [ 527# method: "biomart" 528# type: "P" 529# url: "http://www.biomart.org:80/biomart/martservice" 530# dbalias is the dataset 531# dbalias: "hsapiens_gene_ensembl" 532# 533# The format must be 'biomart' 534# format: "biomart" 535# 536# identifier is the biomart filter the query will be performed with 537# e.g. seqret martensembl:ENST00000380152 538# 539# identifier: "ensembl_transcript_id" 540# 541# Additional filters may be added here e.g. 542# 543# filter: "chromosome_name=13" 544# 545# This is the biomart attribute specifying the sequence 546# 547# sequence: "peptide" 548# 549# These are fields you want returned as part of the description 550# 551# return: "ensembl_gene_id,description,external_gene_id,chromosome_name" 552#] 553 554 555 556#################################################################### 557# SQL example (dummy) 558#################################################################### 559 560#DB sqlexample [ 561# method: "sql" 562# type: "N" 563# 564# method://username:password@host/databasename 565# url: "mysql://dummy:pass@machine.somedomain.org:3306/dummyseqs" 566# 567# dbalias is the table name containing the sequence information 568# dbalias: "sequences" 569# 570# The SQL data is processed using biomart format. That is not a typo. 571# format: "biomart" 572# 573# Column name containing IDs|Accs i.e. the column the query will be 574# performed against 575# identifier: "accession" 576# 577# Any additional SQL restrictions can be put here e.g. 578# filter: "AND version IS NOT NULL" 579# 580# Column containing sequence 581# sequence: "sequence" 582# 583# Columns you want to add to the description 584# return: "version,description" 585#] 586 587 588 589################################################################## 590# Ensembl datatabase access example via public MySQL instances. 591# 592# Please note that these public MySQL instances are only provided 593# for small-scale access. For extended analyses and if in doubt, 594# please copy the relevant databases to a private MySQL instance 595# and configure access accordingly. Please see the following 596# instructions on how to setup your own MySQL server. 597# http://www.ensembl.org/info/docs/webcode/install/build.html 598################################################################## 599 600# DB ensembl [ 601# type: "Nucleotide" 602# format: "ensembl" 603# method: "ensembl" 604# url: "mysql://anonymous:@ensembldb.ensembl.org:5306/" 605# comment: "Ensembl test database" 606# ] 607# 608# DB ensemblgenomes [ 609# type: "Nucleotide" 610# format: "ensembl" 611# method: "ensembl" 612# url: "mysql://anonymous:@mysql.ebi.ac.uk:4157/" 613# comment: "Ensembl test database" 614# ] 615 616 617 618################################################################## 619# Resource definitions for the dbx indexing system. 620################################################################## 621# 622#RES embl [ type: Index 623# idlen: 15 624# acclen: 15 625# svlen: 15 626# keylen: 15 627# deslen: 15 628# orglen: 15 629#] 630