                             ROCON documentation



CONTENTS

   1.0 SUMMARY
   2.0 INPUTS & OUTPUTS
   3.0 INPUT FILE FORMAT
   4.0 OUTPUT FILE FORMAT
   5.0 DATA FILES
   6.0 USAGE
   7.0 KNOWN BUGS & WARNINGS
   8.0 NOTES
   9.0 DESCRIPTION
   10.0 ALGORITHM
   11.0 RELATED APPLICATIONS
   12.0 DIAGNOSTIC ERROR MESSAGES
   13.0 AUTHORS
   14.0 REFERENCES

1.0 SUMMARY

   Reads a DHF file (domain hits file) of hits (sequences of unknown
   structural classification) and a domain families file (validation
   sequences of known classification) and writes a "hits file" for the
   hits, which are classified and rank-ordered on the basis of score.
   Generate a hits file from comparing two DHF files

2.0 INPUTS & OUTPUTS

   ROCON reads a DHF file (domain hits file) of hits generated for a
   single node from a classification hierarchy, e.g. SCOP family. These
   sequences are putatively related to the node in question but are, in
   fact, of unknown classification. ROCON also reads a domain families
   file (in DHF format), containing "validation" sequences (of known
   classification). These sequences are used to classify the input hits. A
   "hits file" (suitable for input into the ROCPLOT application) is
   written, which contains the input hits, classified and rank-ordered on
   the basis of score.

3.0 INPUT FILE FORMAT

   The format of the DHF is described in SEQSEARCH documentation. See also
   the example of the DHF file for hit sequences (Figure 1) and validation
   sequences (Figure 2) below.

  Input files for usage example

  File: rocon/rocon.dhf

> Q9YBD5^.^11^105^SCOP^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^SPARSE^
61.50^0.000e+00^4.000e-10
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNV
IEDYKVVEKVKLKLP
> Q9YBD5^.^95^135^SCOP^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^SPARSE^
11.50^0.000e+00^4.000e-5
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNV
IEDYKVVEKVKLKLP
> Q9YBD5^.^181^235^SCOP^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^SPARSE
^161.50^0.000e+00^4.000e-5
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNV
IEDYKVVEKVKLKLP
> O26938^.^11^101^SCOP^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAS
T^81.90^0.000e+00^3.000e-16
VKPIKNGTVIDHITANRSLNVLNILGLPDGRSKVTVAMNMDSSQLGSKDIVKIENRELKPSEVDQIALIAPRATINIVRD
YKIVEKAKVRL
> Q8Z130^.^8^99^SCOP^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^
181.00^0.000e+00^0.000e+00
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTDEQVNQLALYAPQATVNRIDN
YDVVGKSRPSLP
> Q7MX57^.^8^99^SCOP^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^
80.80^0.000e+00^7.000e-16
VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIRD
YEVVEKRQVEVP
> Q8TVB1^.^7^98^SCOP^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^
72.70^0.000e+00^2.000e-13
VKRIEMGTVLDHLPPGTAPQIMRILDIDPTETTLLVAINVESSKMGRKDILKIEGKILSEEEANKVALVAPNATVNIVRD
YSVAEKFQVKPP
> P96175^.^8^99^SCOP^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^
107.00^0.000e+00^7.000e-24
VEAICNGYVIDHIPSGQGVKILRLFSLTDTKQRVTVGFNLPSHDGTTKDLIKVENTEITKSQANQLALLAPNATVNIIEN
FKVTDKHSLALP

  File: rocon.valid

> Q9YBD5^.^11^105^SCOP^.^1^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^61
.50^0.000e+00^4.000e-10
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNV
IEDYKVVEKVKLKLP
> Q9UX07^.^12^104^SCOP^.^1^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^65
.80^0.000e+00^2.000e-11
VSKIRNGTVIDHIPAGRALAVLRILGIRGSEGYRVALVMNVESKKIGRKDIVKIEDRVIDEKEASLITLIAPSATINIIR
DYVVTEKRHLEVP
> Q9KP65^.^9^100^SCOP^.^1^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^128
.00^0.000e+00^3.000e-30
VEAIKNGTVIDHIPAKVGIKVLKLFDMHNSAQRVTIGLNLPSSALGSKDLLKIENVFISEAQANKLALYAPHATVNQIEN
YEVVKKLALQLP
> Q9K1K9^.^8^99^SCOP^.^1^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^101.
00^0.000e+00^5.000e-22
VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTIDN
FKVVQKRHLNLP
> Q9JWY6^.^8^99^SCOP^.^1^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^98.9
0^0.000e+00^2.000e-21
VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTIDH
FKVVQKRHLNLP
> Q9HKM3^.^7^99^SCOP^.^1^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^79.6
0^0.000e+00^2.000e-15
ISKIRDGTVIDHVPSGKGIRVIGVLGVHEDVNYTVSLAIHVPSNKMGFKDVIKIENRFLDRNELDMISLIAPNATISIIK
NYEISEKFQVELP
> Q9HHN3^.^9^101^SCOP^.^1^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^78.
50^0.000e+00^4.000e-15
VSKIQAGTVIDHIPAGQALQVLQILGTNGASDDQITVGMNVTSERHHRKDIVKIEGRELSQDEVDVLSLIAPDATINIVR
DYEVDEKRRVDRP
> Q97FS4^.^4^93^SCOP^.^2^Class 1^.^.^Fold 1^Superfamily 1^Family 2^PSIBLAST^49.2
0^0.000e+00^2.000e-06
INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDEK
IRQKIQLKLP
> Q97B28^.^8^100^SCOP^.^2^Class 1^.^.^Fold 1^Superfamily 1^Family 2^PSIBLAST^79.
20^0.000e+00^2.000e-15
ISKIKDGTVIDHIPSGKALRVLSILGIRDDVDYTVSVGMHVPSSKMEYKDVIKIENRSLDKNELDMISLTAPNATISIIK
NYEISEKFKVELP
> Q970X3^.^11^101^SCOP^.^2^Class 1^.^.^Fold 1^Superfamily 1^Family 2^PSIBLAST^78
.50^0.000e+00^3.000e-15
VSKIKNGTVIDHIPAGRALAVLRILKIAEGYRIALVMNVESKKMGKKDIVKIENKEVDEKEANLITLIAPTATINIIRDY
EVVEKKKLKIP
> Q8ZTG2^.^7^99^SCOP^.^2^Class 1^.^.^Fold 1^Superfamily 1^Family 2^PSIBLAST^66.1
0^0.000e+00^2.000e-11
VSKIENGTVIDHIPAGRALTVLRILGISGKEGLRVALVMNVESKKLGKKDIVKIEGRELTPEEVNIISAVAPTATINIIR
NFAVVKKFKVTPP
> Q8ZB38^.^9^100^SCOP^.^2^Class 1^.^.^Fold 1^Superfamily 1^Family 2^PSIBLAST^156
.00^0.000e+00^1.000e-38
VEAIKCGTVIDHIPAQIGFKLLSLFKLTATDQRITIGLNLPSKRSGRKDLIKIENTFLTEQQANQLAMYAPDATVNRIDN
YEVVKKLTLSLP
> Q8Z130^.^8^99^SCOP^.^2^Class 1^.^.^Fold 1^Superfamily 1^Family 2^PSIBLAST^181.
00^0.000e+00^0.000e+00
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTDEQVNQLALYAPQATVNRIDN
YDVVGKSRPSLP
> Q8U374^.^6^99^SCOP^.^2^Class 1^.^.^Fold 1^Superfamily 1^Family 2^PSIBLAST^92.0
0^0.000e+00^3.000e-19
VSAIKEGTVIDHIPAGKGLKVIQILGLGELKNGGAVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNII
REYKVVEKFKVEIP
> Q8TVB1^.^7^98^SCOP^.^3^Class 1^.^.^Fold 1^Superfamily 2^Family 1^PSIBLAST^72.7
0^0.000e+00^2.000e-13
VKRIEMGTVLDHLPPGTAPQIMRILDIDPTETTLLVAINVESSKMGRKDILKIEGKILSEEEANKVALVAPNATVNIVRD
YSVAEKFQVKPP
> Q8THL3^.^9^100^SCOP^.^3^Class 1^.^.^Fold 1^Superfamily 2^Family 1^PSIBLAST^69.
20^0.000e+00^2.000e-12
IQAIENGTVIDHITAGQALNVLRILRISSAFRATVSFVMNAPGARGKKDVVKIEGKELSVEELNRIALISPKATINIIRD
FEVVQKNKVVLP
> Q8PXK6^.^9^100^SCOP^.^3^Class 1^.^.^Fold 1^Superfamily 2^Family 1^PSIBLAST^62.
70^0.000e+00^2.000e-10
VQAIESGTVIDHIKSGQALNVLRILGISSAFRATISFVMNAPGAGGKKDVVKIEGKELSVEELNRIALISPKATINIIRD
FVVVQKNNVVLP
> Q8K9H8^.^8^99^SCOP^.^3^Class 1^.^.^Fold 1^Superfamily 2^Family 1^PSIBLAST^146.
00^0.000e+00^1.000e-35
VEAIKSGSVIDHIPAHIGFKLLSLFRFTETEKRITIGLNLPSQKLDKKDIIKIENTFLSDDQINQLAIYAPCATVNYIEK
YNLVGKIFPSLP
> Q8DCF7^.^9^100^SCOP^.^3^Class 1^.^.^Fold 1^Superfamily 2^Family 1^PSIBLAST^127
.00^0.000e+00^9.000e-30
VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIED
YQVVKKLALELP
> Q8D1W6^.^9^100^SCOP^.^4^Class 1^.^.^Fold 1^Superfamily 2^Family 2^PSIBLAST^123
.00^0.000e+00^1.000e-28
VEAIFGGTVIDHIPAQVGLKLLSLFKWLHTKERITMGLNLPSNQQKKKDLIKLENVLLNEDQANQLSIYAPLATVNQIKN
YIVIKKQKLKLP
> Q8A9S4^.^10^101^SCOP^.^4^Class 1^.^.^Fold 1^Superfamily 2^Family 2^PSIBLAST^63
.80^0.000e+00^9.000e-11
VAALKNGTVIDHIPSEKLFTVVQLLGVEQMKCNITIGFNLDSKKLGKKGIIKIADKFFCDEEINRISVVAPYVKLNIIRD
YEVVEKKEVRMP
> Q891I9^.^4^94^SCOP^.^4^Class 1^.^.^Fold 1^Superfamily 2^Family 2^PSIBLAST^52.3
0^0.000e+00^2.000e-07
ITSIKDGIVIDHIKSGYGIKIFNYLNLKNVEYSVALIMNVFSSKLGKKDIIKIANKEIDIDFTVLGLIDPTITINIIEDE
KIKEKLNLELP
> Q87LF7^.^9^100^SCOP^.^4^Class 1^.^.^Fold 1^Superfamily 2^Family 2^PSIBLAST^130
.00^0.000e+00^7.000e-31
VEAIKNGTVIDHIPAQIGIKVLKLFDMHNSSQRVTIGLNLPSSALGHKDLLKIENVFINEEQASKLALYAPHATVNQIEN
YEVVKKLALELP
> Q83IL8^.^8^99^SCOP^.^4^Class 1^.^.^Fold 1^Superfamily 2^Family 2^PSIBLAST^189.
00^0.000e+00^0.000e+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEEQVDQLALYAPQATVNRIDN
YEVVGKSRPSLP
> Q7P144^.^7^98^SCOP^.^4^Class 1^.^.^Fold 1^Superfamily 2^Family 2^PSIBLAST^128.
00^0.000e+00^3.000e-30
VEALKQGTVIDHIPAGEGVKILRLFKLTETGERVTVGLNLVSRHMGSKDLIKVENVALTEEQANELALFAPKATVNVIDN
FEVVKKHKLTLP
> Q7MZ14^.^9^100^SCOP^.^4^Class 1^.^.^Fold 1^Superfamily 2^Family 2^PSIBLAST^150
.00^0.000e+00^6.000e-37
VEAIRCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSNRLGKKDLIKIENTFLTEQQANQLAMYAPNATVNCIEN
YEVVKKLPINLP
> Q7MX57^.^8^99^SCOP^.^5^Class 1^.^.^Fold 2^Superfamily 1^Family 1^PSIBLAST^80.8
0^0.000e+00^7.000e-16
VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIRD
YEVVEKRQVEVP
> Q7MHF0^.^9^100^SCOP^.^5^Class 1^.^.^Fold 2^Superfamily 1^Family 1^PSIBLAST^127
.00^0.000e+00^8.000e-30
VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIED
YQVVKKLALELP
> Q58801^.^9^99^SCOP^.^5^Class 1^.^.^Fold 2^Superfamily 1^Family 1^PSIBLAST^61.5
0^0.000e+00^5.000e-10
VKKITNGTVIDHIDAGKALMVFKVLNVPKETSVMIAINVPSKKKGKKDILKIEGIELKKEDVDKISLISPDVTINIIRNG
KVVEKLKPQIP
> P96175^.^8^99^SCOP^.^5^Class 1^.^.^Fold 2^Superfamily 1^Family 1^PSIBLAST^107.
00^0.000e+00^7.000e-24
VEAICNGYVIDHIPSGQGVKILRLFSLTDTKQRVTVGFNLPSHDGTTKDLIKVENTEITKSQANQLALLAPNATVNIIEN
FKVTDKHSLALP
> P96111^.^375^472^SCOP^.^5^Class 1^.^.^Fold 2^Superfamily 1^Family 1^PSIBLAST^4
7.30^0.000e+00^9.000e-06
GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLPDRYLSKKEIKKLSAISPNTT
VNIIKNSTVVEKYRIKLP
> P77919^.^6^99^SCOP^.^6^Class 1^.^.^Fold 2^Superfamily 1^Family 2^PSIBLAST^93.5
0^0.000e+00^1.000e-19
VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNGGAVLLAMNVPSKKLGRKDIVKVEGRFLSEEEVNKIALVAPNATVNII
RDYKVVEKFKVEVP
> P74766^.^12^104^SCOP^.^6^Class 1^.^.^Fold 2^Superfamily 1^Family 2^PSIBLAST^74
.20^0.000e+00^7.000e-14
VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEGFRIALVINVDSKKMGKKDIVKIEDKEISDTEANLITLIAPTATINIVR
EYEVVKKTKLEVP
> P57451^.^8^99^SCOP^.^7^Class 1^.^.^Fold 2^Superfamily 2^Family 1^PSIBLAST^143.
00^0.000e+00^1.000e-34
VEAIKSGSVIDHIPEYIGFKLLSLFRFTETEKRITIGLNLPSKKLGRKDIIKIENTFLSDEQINQLAIYAPHATVNYINE
YNLVRKVFPTLP
> P19936^.^8^99^SCOP^.^7^Class 1^.^.^Fold 2^Superfamily 2^Family 1^PSIBLAST^159.
00^0.000e+00^1.000e-39
VEAIKCGTVIDHIPAQIGFKLLTLFKLTATDQRITIGLNLPSNELGRKDLIKIENTFLTEQQANQLAMYAPKATVNRIDN
YEVVRKLTLSLP
> P08421^.^8^99^SCOP^.^7^Class 1^.^.^Fold 2^Superfamily 2^Family 1^PSIBLAST^183.
00^0.000e+00^0.000e+00
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTEEQVNQLALYAPQATVNRIDN
YDVVGKSRPSLP
> P00478^.^8^99^SCOP^.^8^Class 1^.^.^Fold 2^Superfamily 2^Family 2^PSIBLAST^191.
00^0.000e+00^0.000e+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDN
YEVVGKSRPSLP
> O58452^.^6^99^SCOP^.^8^Class 1^.^.^Fold 2^Superfamily 2^Family 2^PSIBLAST^94.3
0^0.000e+00^6.000e-20
VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNGGSVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNII
RNYKVVEKFKVEVP
> O30129^.^6^98^SCOP^.^9^Class 2^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^79.6
0^0.000e+00^2.000e-15
VSKIKEGTVIDHINAGKALLVLKILKIQPGTDLTVSMAMNVPSSKMGKKDIVKVEGMFIRDEELNKIALISPNATINLIR
DYEIERKFKVSPP
> O26938^.^11^101^SCOP^.^10^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^8
1.90^0.000e+00^3.000e-16
VKPIKNGTVIDHITANRSLNVLNILGLPDGRSKVTVAMNMDSSQLGSKDIVKIENRELKPSEVDQIALIAPRATINIVRD
YKIVEKAKVRL

   <--
   Figure 1 Excerpt of DHF file (hit sequences)

> Q9YBD5^.^11^105^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^SPARSE^61.50
^0.000e+00^4.000e-10
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNV
IEDYKVVEKVKLKLP
> Q9YBD5^.^95^135^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^SPARSE^11.50
^0.000e+00^4.000e-5
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNV
IEDYKVVEKVKLKLP
> Q9YBD5^.^181^235^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^SPARSE^161.
50^0.000e+00^4.000e-5
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNV
IEDYKVVEKVKLKLP
> O26938^.^11^101^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^81.
90^0.000e+00^3.000e-16
VKPIKNGTVIDHITANRSLNVLNILGLPDGRSKVTVAMNMDSSQLGSKDIVKIENRELKPSEVDQIALIAPRATINIVRD
YKIVEKAKVRL
> Q8Z130^.^8^99^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^181.0
0^0.000e+00^0.000e+00
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTDEQVNQLALYAPQATVNRIDN
YDVVGKSRPSLP
> Q7MX57^.^8^99^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^80.80
^0.000e+00^7.000e-16
VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIRD
YEVVEKRQVEVP
> Q8TVB1^.^7^98^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^72.70
^0.000e+00^2.000e-13
VKRIEMGTVLDHLPPGTAPQIMRILDIDPTETTLLVAINVESSKMGRKDILKIEGKILSEEEANKVALVAPNATVNIVRD
YSVAEKFQVKPP
> P96175^.^8^99^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^107.0
0^0.000e+00^7.000e-24
VEAICNGYVIDHIPSGQGVKILRLFSLTDTKQRVTVGFNLPSHDGTTKDLIKVENTEITKSQANQLALLAPNATVNIIEN
FKVTDKHSLALP

   Figure 1 Excerpt of domain families file (validation sequences)

> Q9YBD5^.^11^105^.^1^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^61.50^0
.000e+00^4.000e-10
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNV
IEDYKVVEKVKLKLP
> Q9UX07^.^12^104^.^1^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^65.80^0
.000e+00^2.000e-11
VSKIRNGTVIDHIPAGRALAVLRILGIRGSEGYRVALVMNVESKKIGRKDIVKIEDRVIDEKEASLITLIAPSATINIIR
DYVVTEKRHLEVP
> Q9KP65^.^9^100^.^1^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^128.00^0
.000e+00^3.000e-30
VEAIKNGTVIDHIPAKVGIKVLKLFDMHNSAQRVTIGLNLPSSALGSKDLLKIENVFISEAQANKLALYAPHATVNQIEN
YEVVKKLALQLP
> Q9K1K9^.^8^99^.^1^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^101.00^0.
000e+00^5.000e-22
VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTIDN
FKVVQKRHLNLP
> Q9JWY6^.^8^99^.^1^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^98.90^0.0
00e+00^2.000e-21
VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTIDH
FKVVQKRHLNLP
> Q9HKM3^.^7^99^.^1^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^79.60^0.0
00e+00^2.000e-15
ISKIRDGTVIDHVPSGKGIRVIGVLGVHEDVNYTVSLAIHVPSNKMGFKDVIKIENRFLDRNELDMISLIAPNATISIIK
NYEISEKFQVELP
> Q9HHN3^.^9^101^.^1^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^78.50^0.
000e+00^4.000e-15
VSKIQAGTVIDHIPAGQALQVLQILGTNGASDDQITVGMNVTSERHHRKDIVKIEGRELSQDEVDVLSLIAPDATINIVR
DYEVDEKRRVDRP
> Q97FS4^.^4^93^.^2^Class 1^.^.^Fold 1^Superfamily 1^Family 2^PSIBLAST^49.20^0.0
00e+00^2.000e-06
INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDEK
IRQKIQLKLP
> Q97B28^.^8^100^.^2^Class 1^.^.^Fold 1^Superfamily 1^Family 2^PSIBLAST^79.20^0.
000e+00^2.000e-15
ISKIKDGTVIDHIPSGKALRVLSILGIRDDVDYTVSVGMHVPSSKMEYKDVIKIENRSLDKNELDMISLTAPNATISIIK
NYEISEKFKVELP
> Q970X3^.^11^101^.^2^Class 1^.^.^Fold 1^Superfamily 1^Family 2^PSIBLAST^78.50^0
.000e+00^3.000e-15
VSKIKNGTVIDHIPAGRALAVLRILKIAEGYRIALVMNVESKKMGKKDIVKIENKEVDEKEANLITLIAPTATINIIRDY
EVVEKKKLKIP
> Q8ZTG2^.^7^99^.^2^Class 1^.^.^Fold 1^Superfamily 1^Family 2^PSIBLAST^66.10^0.0
00e+00^2.000e-11
VSKIENGTVIDHIPAGRALTVLRILGISGKEGLRVALVMNVESKKLGKKDIVKIEGRELTPEEVNIISAVAPTATINIIR
NFAVVKKFKVTPP
> Q8ZB38^.^9^100^.^2^Class 1^.^.^Fold 1^Superfamily 1^Family 2^PSIBLAST^156.00^0
.000e+00^1.000e-38
VEAIKCGTVIDHIPAQIGFKLLSLFKLTATDQRITIGLNLPSKRSGRKDLIKIENTFLTEQQANQLAMYAPDATVNRIDN
YEVVKKLTLSLP
> Q8Z130^.^8^99^.^2^Class 1^.^.^Fold 1^Superfamily 1^Family 2^PSIBLAST^181.00^0.
000e+00^0.000e+00
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTDEQVNQLALYAPQATVNRIDN
YDVVGKSRPSLP
> Q8U374^.^6^99^.^2^Class 1^.^.^Fold 1^Superfamily 1^Family 2^PSIBLAST^92.00^0.0
00e+00^3.000e-19
VSAIKEGTVIDHIPAGKGLKVIQILGLGELKNGGAVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNII
REYKVVEKFKVEIP
> Q8TVB1^.^7^98^.^3^Class 1^.^.^Fold 1^Superfamily 2^Family 1^PSIBLAST^72.70^0.0
00e+00^2.000e-13
VKRIEMGTVLDHLPPGTAPQIMRILDIDPTETTLLVAINVESSKMGRKDILKIEGKILSEEEANKVALVAPNATVNIVRD
YSVAEKFQVKPP
> Q8THL3^.^9^100^.^3^Class 1^.^.^Fold 1^Superfamily 2^Family 1^PSIBLAST^69.20^0.
000e+00^2.000e-12
IQAIENGTVIDHITAGQALNVLRILRISSAFRATVSFVMNAPGARGKKDVVKIEGKELSVEELNRIALISPKATINIIRD
FEVVQKNKVVLP
> Q8PXK6^.^9^100^.^3^Class 1^.^.^Fold 1^Superfamily 2^Family 1^PSIBLAST^62.70^0.
000e+00^2.000e-10
VQAIESGTVIDHIKSGQALNVLRILGISSAFRATISFVMNAPGAGGKKDVVKIEGKELSVEELNRIALISPKATINIIRD
FVVVQKNNVVLP
> Q8K9H8^.^8^99^.^3^Class 1^.^.^Fold 1^Superfamily 2^Family 1^PSIBLAST^146.00^0.
000e+00^1.000e-35
VEAIKSGSVIDHIPAHIGFKLLSLFRFTETEKRITIGLNLPSQKLDKKDIIKIENTFLSDDQINQLAIYAPCATVNYIEK
YNLVGKIFPSLP
> Q8DCF7^.^9^100^.^3^Class 1^.^.^Fold 1^Superfamily 2^Family 1^PSIBLAST^127.00^0
.000e+00^9.000e-30
VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIED
YQVVKKLALELP
> Q8D1W6^.^9^100^.^4^Class 1^.^.^Fold 1^Superfamily 2^Family 2^PSIBLAST^123.00^0
.000e+00^1.000e-28
VEAIFGGTVIDHIPAQVGLKLLSLFKWLHTKERITMGLNLPSNQQKKKDLIKLENVLLNEDQANQLSIYAPLATVNQIKN
YIVIKKQKLKLP
> Q8A9S4^.^10^101^.^4^Class 1^.^.^Fold 1^Superfamily 2^Family 2^PSIBLAST^63.80^0
.000e+00^9.000e-11
VAALKNGTVIDHIPSEKLFTVVQLLGVEQMKCNITIGFNLDSKKLGKKGIIKIADKFFCDEEINRISVVAPYVKLNIIRD
YEVVEKKEVRMP
> Q891I9^.^4^94^.^4^Class 1^.^.^Fold 1^Superfamily 2^Family 2^PSIBLAST^52.30^0.0
00e+00^2.000e-07
ITSIKDGIVIDHIKSGYGIKIFNYLNLKNVEYSVALIMNVFSSKLGKKDIIKIANKEIDIDFTVLGLIDPTITINIIEDE
KIKEKLNLELP
> Q87LF7^.^9^100^.^4^Class 1^.^.^Fold 1^Superfamily 2^Family 2^PSIBLAST^130.00^0
.000e+00^7.000e-31
VEAIKNGTVIDHIPAQIGIKVLKLFDMHNSSQRVTIGLNLPSSALGHKDLLKIENVFINEEQASKLALYAPHATVNQIEN
YEVVKKLALELP
> Q83IL8^.^8^99^.^4^Class 1^.^.^Fold 1^Superfamily 2^Family 2^PSIBLAST^189.00^0.
000e+00^0.000e+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEEQVDQLALYAPQATVNRIDN
YEVVGKSRPSLP
> Q7P144^.^7^98^.^4^Class 1^.^.^Fold 1^Superfamily 2^Family 2^PSIBLAST^128.00^0.
000e+00^3.000e-30
VEALKQGTVIDHIPAGEGVKILRLFKLTETGERVTVGLNLVSRHMGSKDLIKVENVALTEEQANELALFAPKATVNVIDN
FEVVKKHKLTLP
> Q7MZ14^.^9^100^.^4^Class 1^.^.^Fold 1^Superfamily 2^Family 2^PSIBLAST^150.00^0
.000e+00^6.000e-37
VEAIRCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSNRLGKKDLIKIENTFLTEQQANQLAMYAPNATVNCIEN
YEVVKKLPINLP
> Q7MX57^.^8^99^.^5^Class 1^.^.^Fold 2^Superfamily 1^Family 1^PSIBLAST^80.80^0.0
00e+00^7.000e-16
VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIRD
YEVVEKRQVEVP
> Q7MHF0^.^9^100^.^5^Class 1^.^.^Fold 2^Superfamily 1^Family 1^PSIBLAST^127.00^0
.000e+00^8.000e-30
VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIED
YQVVKKLALELP
> Q58801^.^9^99^.^5^Class 1^.^.^Fold 2^Superfamily 1^Family 1^PSIBLAST^61.50^0.0
00e+00^5.000e-10
VKKITNGTVIDHIDAGKALMVFKVLNVPKETSVMIAINVPSKKKGKKDILKIEGIELKKEDVDKISLISPDVTINIIRNG
KVVEKLKPQIP
> P96175^.^8^99^.^5^Class 1^.^.^Fold 2^Superfamily 1^Family 1^PSIBLAST^107.00^0.
000e+00^7.000e-24
VEAICNGYVIDHIPSGQGVKILRLFSLTDTKQRVTVGFNLPSHDGTTKDLIKVENTEITKSQANQLALLAPNATVNIIEN
FKVTDKHSLALP
> P96111^.^375^472^.^5^Class 1^.^.^Fold 2^Superfamily 1^Family 1^PSIBLAST^47.30^
0.000e+00^9.000e-06
GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLPDRYLSKKEIKKLSAISPNTT
VNIIKNSTVVEKYRIKLP
> P77919^.^6^99^.^6^Class 1^.^.^Fold 2^Superfamily 1^Family 2^PSIBLAST^93.50^0.0
00e+00^1.000e-19
VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNGGAVLLAMNVPSKKLGRKDIVKVEGRFLSEEEVNKIALVAPNATVNII
RDYKVVEKFKVEVP
> P74766^.^12^104^.^6^Class 1^.^.^Fold 2^Superfamily 1^Family 2^PSIBLAST^74.20^0
.000e+00^7.000e-14
VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEGFRIALVINVDSKKMGKKDIVKIEDKEISDTEANLITLIAPTATINIVR
EYEVVKKTKLEVP
> P57451^.^8^99^.^7^Class 1^.^.^Fold 2^Superfamily 2^Family 1^PSIBLAST^143.00^0.
000e+00^1.000e-34
VEAIKSGSVIDHIPEYIGFKLLSLFRFTETEKRITIGLNLPSKKLGRKDIIKIENTFLSDEQINQLAIYAPHATVNYINE
YNLVRKVFPTLP
> P19936^.^8^99^.^7^Class 1^.^.^Fold 2^Superfamily 2^Family 1^PSIBLAST^159.00^0.
000e+00^1.000e-39
VEAIKCGTVIDHIPAQIGFKLLTLFKLTATDQRITIGLNLPSNELGRKDLIKIENTFLTEQQANQLAMYAPKATVNRIDN
YEVVRKLTLSLP
> P08421^.^8^99^.^7^Class 1^.^.^Fold 2^Superfamily 2^Family 1^PSIBLAST^183.00^0.
000e+00^0.000e+00
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTEEQVNQLALYAPQATVNRIDN
YDVVGKSRPSLP
> P00478^.^8^99^.^8^Class 1^.^.^Fold 2^Superfamily 2^Family 2^PSIBLAST^191.00^0.
000e+00^0.000e+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDN
YEVVGKSRPSLP
> O58452^.^6^99^.^8^Class 1^.^.^Fold 2^Superfamily 2^Family 2^PSIBLAST^94.30^0.0
00e+00^6.000e-20
VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNGGSVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNII
RNYKVVEKFKVEVP
> O30129^.^6^98^.^9^Class 2^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^79.60^0.0
00e+00^2.000e-15
VSKIKEGTVIDHINAGKALLVLKILKIQPGTDLTVSMAMNVPSSKMGKKDIVKVEGMFIRDEELNKIALISPNATINLIR
DYEIERKFKVSPP
> O26938^.^11^101^.^54894^Class 1^.^.^Fold 1^Superfamily 1^Family 1^PSIBLAST^81.
90^0.000e+00^3.000e-16
VKPIKNGTVIDHITANRSLNVLNILGLPDGRSKVTVAMNMDSSQLGSKDIVKIENRELKPSEVDQIALIAPRATINIVRD
YKIVEKAKVRL

   -->

4.0 OUTPUT FILE FORMAT

   The format of the hits file is described in ROCPLOT documentation. See
   also Figure 3.

  Output files for usage example

  File: rocon.hits

> RELATED 8 ; ROC 2
CROSS        Q8Z130    8     99
UNKNOWN      Q9YBD5    181   235
FALSE        P96175    8     99
TRUE         O26938    11    101
FALSE        Q7MX57    8     99
CROSS        Q8TVB1    7     98
TRUE         Q9YBD5    11    105
TRUE         Q9YBD5    95    135

5.0 DATA FILES

   None.

6.0 USAGE

Generate a hits file from comparing two DHF files
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-hitsinfile]        infile     This option specifies the location of the
                                  DHF file (domain hits file) (input). A
                                  'domain hits file' contains database hits
                                  (sequences) with domain classification
                                  information, in the DHF format (FASTA or
                                  EMBL-like). The hits are relatives to a SCOP
                                  or CATH family and are found from a search
                                  of a sequence database. Files containing
                                  hits retrieved by PSIBLAST are generated by
                                  using SEQSEARCH, hits retrieved by a sparse
                                  protein signatare by using SIGSCAN or
                                  various types of HMM and profile by using
                                  LIBSCAN.
  [-validinfile]       infile     This option specifies the name of domain
                                  families file (input). A 'domain families
                                  file' contains sequence relatives (hits) for
                                  each of a number of different SCOP or CATH
                                  families found from searching a sequence
                                  database, e.g. by using SEQSEARCH
                                  (psiblast). The file contains the collated
                                  search results for the indvidual families;
                                  only those hits of unambiguous family
                                  assignment are included. Hits of ambiguous
                                  family assignment are assigned as relatives
                                  to a SCOP or CATH superfamily or fold
                                  instead and are collated into a 'domain
                                  ambiguities file'. The domain families and
                                  ambiguities files are generated by using
                                  SEQSORT and use the same format as a DHF
                                  file (domain hits file).
   -thresh             integer    [10] This option specifies the overlap
                                  threshold for hits. This is the minimum
                                  length (residues) of overlap required for
                                  two hits with the accession number to be
                                  counted as the same hit. The accession
                                  number of the hit, and the start and end
                                  point respectively of the hit relative to
                                  full length sequence are provided in the
                                  lists of hits in the DHF input file. The
                                  overlap is determined from the start and end
                                  points of the hit. For example two hits
                                  with the start and end points of 1-100 and
                                  91-190 respectively are considered to be the
                                  same hit if they have the same accession
                                  numbers and the overlap threshold is 10 or
                                  less. (Any integer value)
   -mode               menu       [1] This option specifies the classification
                                  scheme to use. See ROCON on-line
                                  documentation for more information. (Values:
                                  1 (Family classification scheme); 2 ((Not
                                  yet available)))
  [-hitsoutfile]       outfile    [*.rocon] This option specifies the name of
                                  the hits files (output). A 'hits
                                  file'contains a list of hits (e.g. from a
                                  prediction method) that are classified and
                                  rank-ordered on the basis of score, p-value,
                                  E-value etc. The files generated by using
                                  SIGSCAN and LIBSCAN will contain the results
                                  of a search of a discriminating element
                                  (e.g. hidden Markov model, profile or
                                  signature) against a sequence database. The
                                  ROCPLOT application is run on the files to
                                  perform Receiver Operator Characteristic
                                  (ROC) analysis on the hits.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-hitsoutfile" associated qualifiers
   -odirectory3        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit


  6.1 COMMAND LINE ARGUMENTS

