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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
Extend alignments (DAF file) with sequences (DHF file)
2.0 INPUTS & OUTPUTS
SEQALIGN reads a directory of "seed" alignments and a directory of sets
of protein sequences and writes a directory of "extended" alignments.
An extended alignment is a seed alignment that is extended with
sequences from the appropriate sequence set. The sets directory must
contain a sequence set for each seed alignment directory and the files
must have the same base name. For example, sequences from "family.sets"
are used to extend the seed alignment "family.aln".
Typically, the inputs are (i) DAF files (domain alignment files)
containing structure-based sequence alignments and (ii) DHF files
(domain hits files) containing sequence relatives (of unknown
structure) of these alignments, and the output are DAF files containing
the extended alignments.
The base names of the output alignments are the same as the input
alignments. The paths for input and output files are specified by the
user and the file extensions are set in the ACD file.
3.0 INPUT FILE FORMAT
The format of the domain alignment file is described in DOMAINALIGN
documentation.
If other alignment files are used as input, all of the common file
formats are supported.
The format of the domain hits file is described in SEQSEARCH
documentation.
If other sequence sets are used as input, all of the common file
formats are supported.
4.0 OUTPUT FILE FORMAT
The format of the domain alignment file is described in DOMAINALIGN
documentation. Note however that the file will never contain 'Number'
or 'Post_similar' records. Futhermore, the code before each sequence is
of the form Acc_Start_End (where domain hits files were used as input
sequences) or Acc_n (where other sequences were used as input), where
'Acc' is the accession number of the sequence, 'Start' and 'End' are
the start and end point of the sequence in the full length sequence
respectively, and 'n' is a sequential count of the sequence in the
alignment.
Output files for usage example
File: 54894.daf
# TY SCOP
# XX
# CL Alpha and beta proteins (a+b)
# XX
# FO Ferredoxin-like
# XX
# SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
# XX
# FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
# XX
# SI 54894
# XX
d4at1b1_0 0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPXSGEMG
RKDLIKIE 0
d4at1d1_1 0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPSGXEMG
RKDLIKIE 0
P00478_1_92 0 -VEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPSG-EMG
RKDLIKIE 0
Q83IL8_1_92 0 -VEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPSG-EMG
RKDLIKIE 0
P08421_1_92 0 -VEAIKCGTVIDHIPAQVGFKLLSLFKLTETD----QRITIGLNLPSG-EMG
RKDLIKIE 0
Q8Z130_1_92 0 -VEAIKCGTVIDHIPAQVGFKLLSLFKLTETD----QRITIGLNLPSG-EMG
RKDLIKIE 0
Q8ZB38_1_92 0 -VEAIKCGTVIDHIPAQIGFKLLSLFKLTATD----QRITIGLNLPSK-RSG
RKDLIKIE 0
P19936_1_92 0 -VEAIKCGTVIDHIPAQIGFKLLTLFKLTATD----QRITIGLNLPSN-ELG
RKDLIKIE 0
Q7MZ14_1_92 0 -VEAIRCGTVIDHIPAQVGFKLLSLFKLTETD----QRITIGLNLPSN-RLG
KKDLIKIE 0
Q8K9H8_1_92 0 -VEAIKSGSVIDHIPAHIGFKLLSLFRFTETE----KRITIGLNLPSQ-KLD
KKDIIKIE 0
P57451_1_92 0 -VEAIKSGSVIDHIPEYIGFKLLSLFRFTETE----KRITIGLNLPSK-KLG
RKDIIKIE 0
Q9KP65_1_92 0 -VEAIKNGTVIDHIPAKVGIKVLKLFDMHNSA----QRVTIGLNLPSS-ALG
SKDLLKIE 0
Q87LF7_1_92 0 -VEAIKNGTVIDHIPAQIGIKVLKLFDMHNSS----QRVTIGLNLPSS-ALG
HKDLLKIE 0
Q8DCF7_1_92 0 -VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSS----QRVTIGLNLPSS-ALG
NKDLLKIE 0
Q7MHF0_1_92 0 -VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSS----QRVTIGLNLPSS-ALG
NKDLLKIE 0
Q8D1W6_1_92 0 -VEAIFGGTVIDHIPAQVGLKLLSLFKWLHTK----ERITMGLNLPSN-QQK
KKDLIKLE 0
Q7P144_1_92 0 -VEALKQGTVIDHIPAGEGVKILRLFKLTETG----ERVTVGLNLVSR-HMG
SKDLIKVE 0
P96175_1_92 0 -VEAICNGYVIDHIPSGQGVKILRLFSLTDTK----QRVTVGFNLPSH-DGT
TKDLIKVE 0
Q9K1K9_1_92 0 -VEAIEKGTVIDHIPAGRGLTILRQFKLLHYG----NAVTVGFNLPSK-TQG
SKDIIKIK 0
Q9JWY6_1_92 0 -VEAIEKGTVIDHIPAGRGLTILRQFKLLHYG----NAVTVGFNLPSK-TQG
SKDIIKIK 0
Q970X3_1_91 0 -VSKIKNGTVIDHIPAGRALAVLRILKIAEG-----YRIALVMNVESK-KMG
KKDIVKIE 0
Q9UX07_1_93 0 -VSKIRNGTVIDHIPAGRALAVLRILGIRGSEG---YRVALVMNVESK-KIG
RKDIVKIE 0
P74766_1_93 0 -VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEG---FRIALVINVDSK-KMG
KKDIVKIE 0
Q8ZTG2_1_93 0 -VSKIENGTVIDHIPAGRALTVLRILGISGKEG---LRVALVMNVESK-KLG
KKDIVKIE 0
O58452_1_94 0 -VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNG--GSVLLAMNVPSK-KLG
RKDIVKVE 0
Q8U374_1_94 0 -VSAIKEGTVIDHIPAGKGLKVIQILGLGELKNG--GAVLLAMNVPSK-KLG
RKDIVKVE 0
P77919_1_94 0 -VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNG--GAVLLAMNVPSK-KLG
RKDIVKVE 0
O30129_1_93 0 -VSKIKEGTVIDHINAGKALLVLKILKIQPGTD---LTVSMAMNVPSS-KMG
KKDIVKVE 0
Q8TVB1_1_92 0 -VKRIEMGTVLDHLPPGTAPQIMRILDIDPTET----TLLVAINVESS-KMG
RKDILKIE 0
Q8THL3_1_92 0 -IQAIENGTVIDHITAGQALNVLRILRISSAFR---ATVSFVMNAPGA--RG
KKDVVKIE 0
Q8PXK6_1_92 0 -VQAIESGTVIDHIKSGQALNVLRILGISSAFR---ATISFVMNAPGA--GG
KKDVVKIE 0
Q9HHN3_1_93 0 -VSKIQAGTVIDHIPAGQALQVLQILGTNGASD---DQITVGMNVTSE-RHH
RKDIVKIE 0
Q58801_1_91 0 -VKKITNGTVIDHIDAGKALMVFKVLNVPKETS-----VMIAINVPSK-KKG
KKDILKIE 0
O26938_1_91 0 -VKPIKNGTVIDHITANRSLNVLNILGLPDGRS----KVTVAMNMDSS-QLG
SKDIVKIE 0
Q97B28_1_93 0 -ISKIKDGTVIDHIPSGKALRVLSILGIRDDVD---YTVSVGMHVPSS-KME
YKDVIKIE 0
Q9HKM3_1_93 0 -ISKIRDGTVIDHVPSGKGIRVIGVLGVHEDVN---YTVSLAIHVPSN-KMG
FKDVIKIE 0
Q9YBD5_1_95 0 -VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGY-RWRIAVVINAESS-KLG
RKDILKIE 0
Q7MX57_1_92 0 -VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDK----RITIGNNLRSR-SHG
SKGVIKIE 0
Q8A9S4_1_92 0 -VAALKNGTVIDHIPSEKLFTVVQLLGVEQMKCN----ITIGFNLDSK-KLG
KKGIIKIA 0
Q891I9_1_91 0 -ITSIKDGIVIDHIKSGYGIKIFNYLNLKNVEYS----VALIMNVFSS-KLG
KKDIIKIA 0
Q97FS4_1_90 0 -INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFP----TALIMNAISK-KNK
AKDIIKIE 0
P96111_1_98 0 GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGS
FKGYISLP 0
d4at1b1_0 0 NTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0
d4at1d1_1 0 NTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0
P00478_1_92 0 NTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0
Q83IL8_1_92 0 NTFLSEEQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0
P08421_1_92 0 NTFLTEEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP 0
Q8Z130_1_92 0 NTFLTDEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP 0
Q8ZB38_1_92 0 NTFLTEQQANQLAMYAPDATVNRIDNYEVVKKLTLSLP 0
P19936_1_92 0 NTFLTEQQANQLAMYAPKATVNRIDNYEVVRKLTLSLP 0
Q7MZ14_1_92 0 NTFLTEQQANQLAMYAPNATVNCIENYEVVKKLPINLP 0
Q8K9H8_1_92 0 NTFLSDDQINQLAIYAPCATVNYIEKYNLVGKIFPSLP 0
P57451_1_92 0 NTFLSDEQINQLAIYAPHATVNYINEYNLVRKVFPTLP 0
Q9KP65_1_92 0 NVFISEAQANKLALYAPHATVNQIENYEVVKKLALQLP 0
Q87LF7_1_92 0 NVFINEEQASKLALYAPHATVNQIENYEVVKKLALELP 0
Q8DCF7_1_92 0 NVFINEEQASKLALYAPHATVNQIEDYQVVKKLALELP 0
Q7MHF0_1_92 0 NVFINEEQASKLALYAPHATVNQIEDYQVVKKLALELP 0
Q8D1W6_1_92 0 NVLLNEDQANQLSIYAPLATVNQIKNYIVIKKQKLKLP 0
Q7P144_1_92 0 NVALTEEQANELALFAPKATVNVIDNFEVVKKHKLTLP 0
P96175_1_92 0 NTEITKSQANQLALLAPNATVNIIENFKVTDKHSLALP 0
Q9K1K9_1_92 0 GVCLDDKAADRLALFAPEAVVNTIDNFKVVQKRHLNLP 0
Q9JWY6_1_92 0 GVCLDDKAADRLALFAPEAVVNTIDHFKVVQKRHLNLP 0
Q970X3_1_91 0 NKEVDEKEANLITLIAPTATINIIRDYEVVEKKKLKIP 0
Q9UX07_1_93 0 DRVIDEKEASLITLIAPSATINIIRDYVVTEKRHLEVP 0
P74766_1_93 0 DKEISDTEANLITLIAPTATINIVREYEVVKKTKLEVP 0
Q8ZTG2_1_93 0 GRELTPEEVNIISAVAPTATINIIRNFAVVKKFKVTPP 0
O58452_1_94 0 GKFLSEEEVNKIALVAPTATVNIIRNYKVVEKFKVEVP 0
Q8U374_1_94 0 GKFLSEEEVNKIALVAPTATVNIIREYKVVEKFKVEIP 0
P77919_1_94 0 GRFLSEEEVNKIALVAPNATVNIIRDYKVVEKFKVEVP 0
O30129_1_93 0 GMFIRDEELNKIALISPNATINLIRDYEIERKFKVSPP 0
Q8TVB1_1_92 0 GKILSEEEANKVALVAPNATVNIVRDYSVAEKFQVKPP 0
Q8THL3_1_92 0 GKELSVEELNRIALISPKATINIIRDFEVVQKNKVVLP 0
Q8PXK6_1_92 0 GKELSVEELNRIALISPKATINIIRDFVVVQKNNVVLP 0
Q9HHN3_1_93 0 GRELSQDEVDVLSLIAPDATINIVRDYEVDEKRRVDRP 0
Q58801_1_91 0 GIELKKEDVDKISLISPDVTINIIRNGKVVEKLKPQIP 0
O26938_1_91 0 NRELKPSEVDQIALIAPRATINIVRDYKIVEKAKVRL- 0
Q97B28_1_93 0 NRSLDKNELDMISLTAPNATISIIKNYEISEKFKVELP 0
Q9HKM3_1_93 0 NRFLDRNELDMISLIAPNATISIIKNYEISEKFQVELP 0
Q9YBD5_1_95 0 GYKPRQRDLEVLGIIAPGATFNVIEDYKVVEKVKLKLP 0
Q7MX57_1_92 0 DKTFEEEELNRIALIAPNVRLNIIRDYEVVEKRQVEVP 0
Q8A9S4_1_92 0 DKFFCDEEINRISVVAPYVKLNIIRDYEVVEKKEVRMP 0
Q891I9_1_91 0 NKEIDID-FTVLGLIDPTITINIIEDEKIKEKLNLELP 0
Q97FS4_1_90 0 N--VMDLDLAVLGFLDPNITVNIIEDEKIRQKIQLKLP 0
P96111_1_98 0 DRYLSKKEIKKLSAISPNTTVNIIKNSTVVEKYRIKLP 0
File: 55074.daf
# TY SCOP
# XX
# CL Alpha and beta proteins (a+b)
# XX
# FO Ferredoxin-like
# XX
# SF Adenylyl and guanylyl cyclase catalytic domain
# XX
# FA Adenylyl and guanylyl cyclase catalytic domain
# XX
# SI 55074
# XX
d1cs4a__0 0 MMFHKIYIQKXHXDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
d1fx2a__1 0 XXNNNRAPXKEPTDPVTLIFTDIESSTALWAAX----HPDLMPDAVAAHHRM
VRSLIGR- 0
Q04400_1_189 0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
P40144_1_189 0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
P30803_1_189 0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
O95622_1_189 0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
Q03343_1_189 0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
O43306_1_189 0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
Q01341_1_188 0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
P30804_1_188 0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
Q99279_1_218 0 --NNNRAPKE-PTDPVTLIFTDIESSTALWAA-----HPDLMPDAVAAHHRM
VRSLIGR- 0
Q99280_6_216 0 ---------KEPTGPVTLIFTDIESSTALWAA-----HPDLMPDAVATHHRL
IRSLITR- 0
P26338_1_216 0 ----NNLAPKELTDPVTLIFTDIESSTALWAA-----HPELMPDAVATHHRL
IRSLIGR- 0
Q26721_1_206 0 --------------PVTLIFTDIESSTALWAA-----HPEVMPDAVATHHRL
IRTLISK- 0
Q99396_1_212 0 ---------KELADPVTLIFTDIESSTAQWAT-----QPELMPDAVATHHSM
VRSLIEN- 0
Q08828_1_186 0 --FHKIYIQR--HDNVSILFADIVGFTGLASQC----TAQELVKLLNELFGK
FDELATE- 0
P19754_1_186 0 --FHKIYIQR--HDNVSILFADIVGFTGLASQC----TAQELVKLLNELFGK
FDELATE- 0
P32870_1_186 0 --FHRIYIQK--HENVSILFADIVGFTVLSSQC----SAQELVRLLNELFGR
FDQLAHD- 0
Q26896_6_216 0 ---------KEFTDPVTLIFTDIESSTALWAA-----HPGMMADAVATHHRL
IRSLIAL- 0
P97490_1_186 0 --FHRIYIHR--YENVSILFADVKGFTNLSTTL----SAQELVRMLNELFAR
FDRLAHE- 0
P40146_1_186 0 --FHRIYIHR--YENVSILFADVKGFTNLSTTL----SAQELVRMLNELFAR
FDRLAHE- 0
P40145_1_186 0 --FHRIYIHR--YENVSILFADVKGFTNLSTTL----SAQELVRMLNELFAR
FDRLAHE- 0
Q8VHH7_1_186 0 --FNTMYMYR--HENVSILFADIVGFTQLSSAC----SAQELVKLLNELFAR
FDKLAAK- 0
P21932_1_186 0 --FNTMYMYR--HENVSILFADIVGFTQLSSAC----SAQELVKLLNELFAR
FDKLAAK- 0
O60266_1_186 0 --FNTMYMYR--HENVSILFADIVGFTQLSSAC----SAQELVKLLNELFAR
FDKLAAK- 0
Q27675_1_217 0 ---NNDAAPKDGDEPVTLLFTDIESSTALWAA-----LPQLMSDAIAAHHRV
IRQLVKK- 0
Q25263_1_217 0 ---NNDAAPKDGDEPVTLLFTDIESSTALWAA-----LPQLMSDAIAAHHRV
IRQLVKK- 0
Q91WF3_1_158 0 --FHSLYVKR--HQGVSVLYADIVGFTRLASEC----SPKELVLMLNELFGK
FDQIAKE- 0
Q8NFM4_1_158 0 --FHSLYVKR--HQGVSVLYADIVGFTRLASEC----SPKELVLMLNELFGK
FDQIAKE- 0
P26770_1_158 0 --FHSLYVKR--HQGVSVLYADIVGFTRLASEC----SPKELVLMLNELFGK
FDQIAKE- 0
Q08462_1_186 0 --FHNLYVKR--HTNVSILYADIVGFTRLASDC----SPGELVHMLNELFGK
FDQIAKE- 0
P26769_1_186 0 --FHNLYVKR--HTNVSILYADIVGFTRLASDC----SPGELVHMLNELFGK
FDQIAKE- 0
Q29450_1_186 0 --FHNLYVKR--HQNVSILYADIVGFTRLASDC----SPKELVVVLNELFGK
FDQIAKA- 0
P51829_1_186 0 --FHSLYVKR--HQNVSILYADIVGFTRLASDC----SPKELVVVLNELFGK
FDQIAKA- 0
P51828_1_186 0 --FHSLYVKR--HQNVSILYADIVGFTQLASDC----SPKELVVVLNELFGK
FDQIAKA- 0
P98999_1_150 0 -------------EQVSILFADIVGFTKMSANK----SAHALVGLLNDLFGR
FDRLCEE- 0
Q9DGG6_1_181 0 -------------EQVSILFADIVGFTKMSANK----SAHALVGLLNDLFGR
FDRLCED- 0
P51830_1_179 0 ---------------VSILFADIVGFTKMSANK----SAHALVGLLNDLFGR
FDRLCEQ- 0
[Part of this file has been deleted for brevity]
P40144_1_159 0 ---------------------- 0
P30803_1_159 0 ---------------------- 0
O95622_1_159 0 ---------------------- 0
Q03343_1_159 0 ---------------------- 0
Q01341_1_159 0 ---------------------- 0
P30804_1_159 0 ---------------------- 0
O43306_1_159 0 ---------------------- 0
P97490_1_162 0 ---------------------- 0
P40146_1_162 0 ---------------------- 0
P40145_1_162 0 ---------------------- 0
O30820_1_149 0 ---------------------- 0
Q03101_1_149 0 ---------------------- 0
P16065_1_143 0 ---------------------- 0
P46197_1_168 0 ---------------------- 0
P20594_1_168 0 ---------------------- 0
P16067_1_168 0 ---------------------- 0
P18293_1_168 0 ---------------------- 0
P18910_1_168 0 ---------------------- 0
P16066_1_168 0 ---------------------- 0
P55202_1_154 0 ---------------------- 0
Q07553_1_152 0 ---------------------- 0
Q02846_1_152 0 ---------------------- 0
P52785_1_150 0 ---------------------- 0
P51840_1_150 0 ---------------------- 0
O19179_1_150 0 ---------------------- 0
P55203_1_151 0 ---------------------- 0
P51842_1_152 0 ---------------------- 0
P51841_1_152 0 ---------------------- 0
O02740_1_162 0 ---------------------- 0
P51839_1_163 0 ---------------------- 0
P55204_1_150 0 ---------------------- 0
P25092_1_150 0 ---------------------- 0
P70106_1_150 0 ---------------------- 0
P23897_1_150 0 ---------------------- 0
P55205_1_154 0 ---------------------- 0
Q09435_1_161 0 ---------------------- 0
P22717_1_147 0 ---------------------- 0
O75343_1_147 0 ---------------------- 0
Q9WVI4_1_149 0 ---------------------- 0
P33402_1_149 0 ---------------------- 0
Q9ERL9_1_152 0 ---------------------- 0
P19686_1_160 0 ---------------------- 0
Q02108_1_160 0 ---------------------- 0
P19687_1_161 0 ---------------------- 0
Q07093_1_158 0 ---------------------- 0
Q02153_1_165 0 ---------------------- 0
P20595_1_165 0 ---------------------- 0
P16068_1_165 0 ---------------------- 0
P40137_1_139 0 ---------------------- 0
P23466_1_154 0 ---------------------- 0
File: seqalign.log
//
/homes/user/test/qa/domainalign-keep/daf/54894.daf
//
/homes/user/test/qa/domainalign-keep/daf/55074.daf
5.0 DATA FILES
SEQALIGN does not use a data file.
6.0 USAGE
6.1 COMMAND LINE ARGUMENTS
Extend alignments (DAF file) with sequences (DHF file).
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers (* if not always prompted):
-mode menu [1] This option specifies the mode of
SEQALIGN operation. SEQALIGN takes as input
a directory of either i. single sequences,
ii. set of sequences (unaligned or aligned,
but typically aligned sequences within a
domain alignment file)). The user has to
specify which. (Values: 1 (Single
sequences); 2 (Multiple sequences (e.g.
sequence set or alignment)))
* -dhfinpath dirlist [./] This option specifies the location of
sequences, e.g. DHF files (domain hits
files) (input). SEQALIGN takes as input a
database of either i. single sequences, ii.
sets of unaligned sequences or iii. sets of
aligned sequences, e.g. a domain alignment
file. A 'domain alignment file' contains a
sequence alignment of domains belonging to
the same SCOP or CATH family. The file is in
clustal format annotated with domain family
classification information. The files
generated by using SCOPALIGN will contain a
structure-based sequence alignment of
domains of known structure only. Such
alignments can be extended with sequence
relatives (of unknown structure) by using
SEQALIGN.
* -dafinpath dirlist [./] This option specifies the location of
sequences, e.g. DAF files (domain alignment
files) (input). SEQALIGN takes as input a
database of either i. single sequences, ii.
sets of unaligned sequences or iii. sets of
aligned sequences, e.g. a domain alignment
file. A 'domain alignment file' contains a
sequence alignment of domains belonging to
the same SCOP or CATH family. The file is in
clustal format annotated with domain family
classification information. The files
generated by using SCOPALIGN will contain a
structure-based sequence alignment of
domains of known structure only. Such
alignments can be extended with sequence
relatives (of unknown structure) by using
SEQALIGN.
[-dhfindir] directory [./] This option specifies the location of
DHF files (domain hits files) (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.
-amode menu [1] This option specifies which alignment
algorithm to use. (Values: 1 (CLUSTALW); 2
(TCOFFEE (not yet implemented)))
[-dafoutdir] outdir [./] This option specifies the location of
DAF files (domain alignment files) (output).
A 'domain alignment file' contains a
sequence alignment of domains belonging to
the same SCOP or CATH family. The file is in
clustal format annotated with domain family
classification information. The files
generated by using SCOPALIGN will contain a
structure-based sequence alignment of
domains of known structure only. Such
alignments can be extended with sequence
relatives (of unknown structure) by using
SEQALIGN.
-logfile outfile [seqalign.log] This option specifies the
name of log file for the build. The log file
contains messages about any errors arising
while SEQALIGN ran.
Additional (Optional) qualifiers:
-forcetype boolean [N] This option specifies whether to force
minimal domain classification data to be
written to the output file in cases where
singlet sequences were given as input file
and no classification data was available
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-dhfinpath" associated qualifiers
-extension string Default file extension
"-dafinpath" associated qualifiers
-extension string Default file extension
"-dhfindir" associated qualifiers
-extension1 string Default file extension
"-dafoutdir" associated qualifiers
-extension2 string Default file extension
"-logfile" associated qualifiers
-odirectory 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
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