                                  eomegash



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Sequence with HMM (ClustalO wrapper)

Description

   eomegash is a wrapper to clustalo. It takes a set of unaligned
   sequences and one HMM and produces a combined output alignment.

   Clustal-Omega (clustalo) is a general purpose multiple sequence
   alignment (MSA) program for proteins. It produces high quality MSAs and
   is capable of handling data-sets of hundreds of thousands of sequences
   in reasonable time.

   In its current form Clustal-Omega can only align protein sequences but
   not DNA/RNA sequences. It is envisioned that DNA/RNA will become
   available in a future version.

Algorithm

   Clustal-Omega uses HMMs for the alignment engine, based on the HHalign
   package from Johannes Soeding [1]. Guide trees are optionally made
   using mBed [2] which can cluster very large numbers of sequences in
   O(N*log(N)) time. Multiple alignment then proceeds by aligning larger
   and larger alignments using HHalign, following the clustering given by
   the guide tree.

Usage

   Here is a sample session with eomegash


% eomegash ../data/globins4.hmm
Sequence with HMM (ClustalO wrapper)
(aligned) output sequence set [twoglob.aln]:


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

Sequence with HMM (ClustalO wrapper)
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequences]         seqset     File containing sequences to align
  [-hmmfile]           infile     Pre-aligned multiple sequence file (aligned
                                  columns will be kept fixed)
  [-outseq]            seqoutset  [.] Sequence set filename
                                  and optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -indistfile         infile     Pairwise distance matrix input file (skips
                                  distance computation)
   -inguidefile        infile     Guide tree input file (skips distance
                                  computation and guide tree clustering step)
   -dealign            toggle     [N] Dealign input sequences
   -cluster            menu       [mbed] Method (Values: mbed (mBED method);
                                  full (Full slow method); iter (Iteration
                                  used full slower method))
   -maxiterations      integer    [0] Number of (combined guide tree/HMM)
                                  iterations (Integer from 0 to 2000000000)
   -maxgiterations     integer    [2000000000] Maximum guide tree iterations
                                  (Integer from 0 to 2000000000)
   -maxhiterations     integer    [2000000000] Maximum number of HMM
                                  iterations (Integer from 0 to 2000000000)
   -maxseqs            integer    [2000000000] Maximum number of sequences
                                  (Integer from 2 to 2000000000)
   -maxlenseq          integer    [2000000000] Maximum length of sequence
                                  (Integer from 1 to 2000000000)
   -self               toggle     [N] Set options automatically (might
                                  overwrite some options
   -outformat          menu       [fasta] Format (Values: fasta (FASTA);
                                  clustal (Aln clustal); msf (MSF); phylip
                                  (Phylip); selex (Selex); stockholm
                                  (Stockholm); vienna (ViennaRNA))
   -outdistfile        outfile    [*.eomegash] Pairwise distance matrix output
                                  file, only available in cluster mode 'full'
   -outguidefile       outfile    [*.eomegash] Guide tree output file
   -log                toggle     [N] Log progress to standard output if not
                                  used for output

   Associated qualifiers:

   "-sequences" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outseq" associated qualifiers
   -osformat3          string     Output seq format
   -osextension3       string     File name extension
   -osname3            string     Base file name
   -osdirectory3       string     Output directory
   -osdbname3          string     Database name to add
   -ossingle3          boolean    Separate file for each entry
   -oufo3              string     UFO features
   -offormat3          string     Features format
   -ofname3            string     Features file name
   -ofdirectory3       string     Output directory

   "-outdistfile" associated qualifiers
   -odirectory         string     Output directory

   "-outguidefile" 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


Input file format

   eomegash reads a set of unaligned sequences and optional distance and
   guide tree files.

  Input files for usage example

  File: twoglob.fasta

>HBA_HUMAN P69905 Hemoglobin subunit alpha (Alpha-globin) (Hemoglobin alpha chai
n)
MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG
KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP
AVHASLDKFLASVSTVLTSKYR
>HBA_BOVFRAG Hemoglobin subunit alpha (Alpha-globin) fragment (Hemoglobin alpha
chain)
DKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG
AKVAAALTKAVEHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTP
AVHASLDKFLANVST

  File: globins4.hmm

HMMER3/b [3.0 | March 2010]
NAME  globins4
LENG  149
ALPH  amino
RF    no
CS    no
MAP   yes
DATE  Mon Jul 15 12:00:00 2013
NSEQ  4
EFFN  0.964844
CKSUM 2027839109
STATS LOCAL MSV       -9.9014  0.70957
STATS LOCAL VITERBI  -10.7224  0.70957
STATS LOCAL FORWARD   -4.1637  0.70957
HMM          A        C        D        E        F        G        H        I
     K        L        M        N        P        Q        R        S        T
      V        W        Y
            m->m     m->i     m->d     i->m     i->i     d->m     d->d
  COMPO   2.36553  4.52577  2.96709  2.70473  3.20818  3.02239  3.41069  2.90041
  2.55332  2.35210  3.67329  3.19812  3.45595  3.16091  3.07934  2.66722  2.8547
5  2.56965  4.55393  3.62921
          2.68640  4.42247  2.77497  2.73145  3.46376  2.40504  3.72516  3.29302
  2.67763  2.69377  4.24712  2.90369  2.73719  3.18168  2.89823  2.37879  2.7749
7  2.98431  4.58499  3.61525
          0.57544  1.78073  1.31293  1.75577  0.18968  0.00000        *
      1   1.70038  4.17733  3.76164  3.36686  3.72281  3.29583  4.27570  2.40482
  3.29230  2.54324  3.63799  3.55099  3.93183  3.61602  3.56580  2.71897  2.8410
4  1.67328  5.32720  4.10031      9 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.03156  3.86736  4.58970  0.61958  0.77255  0.34406  1.23405
      2   2.62748  4.47174  3.31917  2.82619  3.63815  3.49607  2.75382  3.03401
  2.75280  2.74783  3.65114  3.24714  2.62341  3.12082  3.11124  2.79244  2.8935
5  1.88003  5.06315  3.77128     10 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
      3   3.50771  4.88753  4.66754  4.31907  3.27776  4.35743  4.88268  2.50779
  4.08449  0.57907  3.22569  4.56607  4.74802  4.37991  4.20749  3.97946  3.7919
1  2.62059  5.25407  4.04279     11 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
      4   2.34080  4.28719  3.51550  3.22063  4.37406  3.06195  4.29366  3.74891
  3.24370  3.47337  4.31943  3.39310  3.80273  3.56072  3.55390  1.08280  2.0028
0  3.23325  5.72380  4.49519     12 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
      5   2.04218  4.87966  2.77126  1.92448  4.32563  3.33660  3.78415  3.73388
  2.61886  3.34029  4.16568  2.96714  2.18012  2.94561  3.07633  2.70238  2.9680
3  3.36068  5.56791  4.21854     13 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
      6   1.67844  4.79514  2.78469  2.00544  4.34945  2.26719  3.85010  3.76260
  2.72087  3.37961  4.20641  2.99947  3.85561  3.02442  3.17766  2.68798  2.9657
5  3.36703  5.60901  4.27005     14 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
      7   3.05756  5.63998  1.78612  1.06702  4.93093  3.31407  3.86695  4.45859
  2.89031  3.95237  4.80915  2.77798  3.94091  3.03432  3.48933  2.93505  3.3481
0  4.02575  6.09427  4.58708     15 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
      8   2.98085  4.92154  3.50401  2.91209  3.76425  3.70161  3.75301  3.57060
  1.24921  3.12012  4.04714  3.32210  4.09411  3.00014  2.54951  3.05147  3.1898
2  3.31354  2.52964  3.70813     16 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
      9   2.59353  4.69451  3.03503  2.60972  4.18917  3.33498  3.80536  3.60013
  2.58953  3.21847  4.04944  3.07115  3.85428  2.20828  2.99231  2.14672  1.8475
3  3.23346  5.45458  4.14691     17 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
     10   2.23880  4.76665  3.06952  2.55248  4.02235  3.47005  3.69787  3.40277
  2.01551  2.36330  3.87991  2.51243  3.88223  2.86967  2.84293  2.72413  2.9030
0  3.10205  5.29826  3.99496     18 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
     11   3.19694  4.48391  4.99800  4.51340  3.70437  4.59686  5.22508  1.39091
  4.40799  2.19554  3.49619  4.71017  4.90059  4.67186  4.59646  3.99910  3.4652
8  0.94853  5.69937  4.48740     19 - -


  [Part of this file has been deleted for brevity]

          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
    134   2.87148  5.44150  1.98118  1.74899  4.74617  3.33260  3.73791  4.25433
  2.62738  3.72942  4.52187  2.07888  3.87291  2.23146  3.17389  2.78299  3.1312
2  3.81624  5.87307  4.40314    150 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
    135   3.27331  5.22456  3.46754  3.04631  4.68046  3.71770  3.96365  4.13172
  0.69147  3.63653  4.59195  3.45354  4.20521  3.14539  2.53832  3.30173  3.5091
5  3.82642  5.61930  4.48069    151 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
    136   2.13728  4.25596  4.26822  3.70038  2.51560  3.93283  4.27242  2.28282
  3.58922  1.68324  3.19522  3.92448  4.28790  3.80594  3.78003  3.23864  3.0440
1  1.82614  4.90639  3.70545    152 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
    137   3.25266  4.59255  4.86528  4.29758  3.18898  4.50160  4.83534  2.17302
  4.15958  1.11276  2.09173  4.53148  4.72252  4.28685  4.28308  3.84128  3.4796
3  1.79006  5.20435  4.12672    153 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
    138   1.79466  4.79782  2.82404  1.94090  4.31166  3.30608  3.81075  3.72422
  2.65702  3.33717  4.15830  2.99339  3.84716  2.97720  3.11199  2.03142  2.9394
9  3.33667  5.56525  4.22435    154 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
    139   2.58506  4.29342  3.55405  3.00981  3.47023  2.68992  3.90060  2.80129
  2.93915  2.04902  2.51305  3.37662  3.96778  3.25166  3.26632  2.35763  2.8450
1  2.57968  4.93542  3.70537    155 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
    140   3.08583  4.40689  4.84510  4.29544  2.25790  4.37874  4.73777  1.57472
  4.17210  1.94826  3.22641  4.44953  4.66205  4.33233  4.29141  3.72292  3.3261
7  1.35939  5.16135  3.94030    156 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
    141   2.02979  2.61338  3.45168  2.91840  3.84883  3.32836  3.92100  3.21873
  2.81248  2.91084  3.77423  3.27409  3.86642  3.17756  2.28029  2.17107  2.8203
2  2.90332  5.22633  3.98297    157 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
    142   2.65037  4.69800  3.11777  2.58559  3.93396  3.48363  3.71066  2.49275
  2.05906  2.95516  3.80693  2.50024  3.88815  2.89605  2.88872  2.72907  2.4276
3  2.99850  5.24239  3.94877    158 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
    143   2.21701  4.52657  2.45380  2.75014  3.73535  3.53805  3.84294  2.86807
  2.75770  2.17002  3.64455  3.21159  3.95457  3.08148  3.16791  2.80094  2.8960
8  2.24528  5.16549  3.89225    159 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
    144   3.41438  4.70993  5.04893  4.51836  3.21871  4.71073  5.05993  1.60681
  4.34794  0.90468  3.01922  4.76098  4.89446  4.48359  4.45935  4.09339  3.6465
9  2.14279  5.32906  4.22624    160 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
    145   1.66341  4.55765  3.29747  2.78822  4.09563  3.34088  3.86205  3.44543
  2.60980  3.11452  3.96692  3.19039  3.87148  3.05878  2.16675  2.67137  2.2904
3  3.09965  5.38848  4.12438    161 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
    146   1.96741  4.60402  3.09101  2.67267  4.09875  3.30287  2.64764  3.55483
  2.68845  3.18630  4.02165  3.11035  3.84730  3.04694  3.09548  1.72418  2.8800
8  3.18467  5.41006  4.09565    162 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
    147   2.02427  4.88556  3.14956  2.70898  4.40362  3.45865  3.80224  3.73109
  1.30907  3.34916  4.21424  3.15279  3.95761  2.96243  2.65527  2.83485  3.0657
3  3.38348  5.54009  4.27566    163 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.02321  4.17053  4.89288  0.61958  0.77255  0.48576  0.95510
    148   3.70647  5.07328  4.29292  4.08736  2.37118  4.18885  3.80078  3.67800
  3.93734  3.05218  4.32316  4.11065  4.65987  4.16910  4.05541  3.80923  3.9969
3  3.56378  4.02310  0.58497    164 - -
          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354
  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.7751
9  2.98518  4.58477  3.61503
          0.19360  4.17053  1.82902  0.61958  0.77255  0.48576  0.95510
    149   2.92198  5.11574  3.28049  2.65489  4.47826  3.59727  2.51142  3.88373
  1.57593  3.35205  4.19259  3.10178  3.96579  2.72398  1.84611  2.91372  3.1036
3  3.55066  5.42147  4.18835    165 - -
          2.68634  4.42241  2.77536  2.73098  3.46370  2.40469  3.72511  3.29370
  2.67757  2.69331  4.24706  2.90363  2.73756  3.18097  2.89817  2.37903  2.7753
6  2.98535  4.58493  3.61418
          0.22163  1.61553        *  1.50361  0.25145  0.00000        *
//

Output file format

   eomegash writes alignments using the default Clustal-Omega output.

  Output files for usage example

  File: twoglob.aln

>HBA_HUMAN P69905 Hemoglobin subunit alpha (Alpha-globin) (Hemoglobin alpha chai
n)
MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG
KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP
AVHASLDKFLASVSTVLTSKYR
>HBA_BOVFRAG Hemoglobin subunit alpha (Alpha-globin) fragment (Hemoglobin alpha
chain)
------DKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG
AKVAAALTKAVEHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTP
AVHASLDKFLANVST-------

Data files

   None.

Notes

   None.

References

   [1] Johannes Soding (2005) Protein homology detection by HMM-HMM
   comparison. Bioinformatics 21 (7): 951aEUR"960.

   [2] Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence
   embedding for fast construction of guide trees for multiple sequence
   alignment. Algorithms Mol Biol. 2010 May 14;5:21.

   [3] http://www.genetics.wustl.edu/eddy/software/#squid

   [4] Wilbur and Lipman, 1983; PMID 6572363

   [5] Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving
   the sensitivity of progressive multiple sequence alignment through
   sequence weighting, position-specific gap penalties and weight matrix
   choice. Nucleic Acids Res., 22, 4673-4680.

   [6] Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA,
   McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD,
   Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0.
   Bioinformatics, 23, 2947-2948.

   [7] Kimura M (1980). "A simple method for estimating evolutionary rates
   of base substitutions through comparative studies of nucleotide
   sequences". Journal of Molecular Evolution 16: 111aEUR"120.

   [8] Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high
   accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name     Description
   edialign         Local multiple alignment of sequences
   emma             Multiple sequence alignment (ClustalW wrapper)
   eomega           Multiple sequence alignment (ClustalO wrapper)
   eomegapp         Profile with profile (ClustalO wrapper)
   eomegaps         Single sequence with profile (ClustalO wrapper)
   eomegasp         Sequence with profile (ClustalO wrapper)
   infoalign        Display basic information about a multiple sequence alignment
   mse              Multiple sequence editor
   plotcon          Plot conservation of a sequence alignment
   prettyplot       Draw a sequence alignment with pretty formatting
   showalign        Display a multiple sequence alignment in pretty format
   tranalign        Generate an alignment of nucleic coding regions from aligned
                    proteins

Author(s)

   Alan Bleasby
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
