infoalign.txt

emboss的linux版本的源代码

HBA_HUMAN     3 72
HBA_HORSE     3 72
MYG_PHYCA     4 108
GLB5_PETMA    2 101
LGB2_LUPLU    0 110

  Output files for usage example 5

  File: globins.infoalign

HBB_HUMAN     3
HBB_HORSE     3
HBA_HUMAN     2
HBA_HORSE     2
MYG_PHYCA     3
GLB5_PETMA    1
LGB2_LUPLU    0

  Output files for usage example 6

  File: globins.infoalign

<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>USA</th><th>Name</th><th>Sequence Length</th><th>Aligned Length</th><th
>Gaps</th><th>Gap Length</th><th>Identity</th><th>Similarity</th><th>Difference
</th><th>% Change</th><th>Weight</th><th>Description</th></tr>
<tr><td>msf::../../data/globins.msf:HBB_HUMAN</td>
<td>HBB_HUMAN</td>
<td>146</td>
<td>150</td>
<td>3</td>
<td>4</td>
<td>68</td>
<td>17</td>
<td>61</td>
<td>54.666668</td>
<td>0.610000</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:HBB_HORSE</td>
<td>HBB_HORSE</td>
<td>146</td>
<td>150</td>
<td>3</td>
<td>4</td>
<td>68</td>
<td>17</td>
<td>61</td>
<td>54.666668</td>
<td>0.650000</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:HBA_HUMAN</td>
<td>HBA_HUMAN</td>
<td>141</td>
<td>144</td>
<td>2</td>
<td>3</td>
<td>60</td>
<td>9</td>
<td>72</td>
<td>58.333332</td>
<td>0.650000</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:HBA_HORSE</td>
<td>HBA_HORSE</td>
<td>141</td>
<td>144</td>
<td>2</td>
<td>3</td>
<td>63</td>
<td>6</td>
<td>72</td>
<td>56.250000</td>
<td>0.830000</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:MYG_PHYCA</td>
<td>MYG_PHYCA</td>
<td>153</td>
<td>157</td>
<td>3</td>
<td>4</td>
<td>30</td>
<td>15</td>
<td>108</td>
<td>80.891716</td>
<td>1.000000</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:GLB5_PETMA</td>
<td>GLB5_PETMA</td>
<td>149</td>
<td>151</td>
<td>1</td>
<td>2</td>
<td>32</td>
<td>16</td>
<td>101</td>
<td>78.807945</td>
<td>0.910000</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:LGB2_LUPLU</td>
<td>LGB2_LUPLU</td>
<td>153</td>
<td>153</td>
<td>0</td>
<td>0</td>
<td>19</td>
<td>24</td>
<td>110</td>
<td>87.581696</td>
<td>0.430000</td>
<td></td>
</tr>
</table>

  Output files for usage example 7

  File: globins.infoalign

# USA             Name        SeqLen    AlignLen        Gaps    GapLen  Ident
Similar Differ  % Change        Weight  Description
msf::../../data/globins.msf:HBB_HUMAN   HBB_HUMAN     146       150     3
4       146     0       0       2.666667        0.610000
msf::../../data/globins.msf:HBB_HORSE   HBB_HORSE     146       150     3
4       122     10      14      18.666666       0.650000
msf::../../data/globins.msf:HBA_HUMAN   HBA_HUMAN     141       144     2
3       48      19      74      66.666664       0.650000
msf::../../data/globins.msf:HBA_HORSE   HBA_HORSE     141       144     2
3       51      18      72      64.583336       0.830000
msf::../../data/globins.msf:MYG_PHYCA   MYG_PHYCA     153       157     3
4       30      22      101     80.891716       1.000000
msf::../../data/globins.msf:GLB5_PETMA  GLB5_PETMA    149       151     1
2       24      27      98      84.105957       0.910000
msf::../../data/globins.msf:LGB2_LUPLU  LGB2_LUPLU    153       153     0
0       21      28      104     86.274513       0.430000

  Output files for usage example 8

  File: test.out

# USA             Name        SeqLen    AlignLen        Gaps    GapLen  Ident
Similar Differ  % Change        Weight  Description
tembl-id:ECLAC    ECLAC         7477    7477    0       0       374     0
7103    94.997993       1.000000        E.coli lactose operon with lacI, lacZ,
lacY and lacA genes.
tembl-id:ECLACA   ECLACA        1832    1832    0       0       374     0
1458    79.585152       1.000000        Escherichia coli lacA gene for thiogala
ctoside transacetylase
tembl-id:ECLACI   ECLACI        1113    1113    0       0       302     0
811     72.866127       1.000000        E. coli laci gene (codes for the lac re
pressor).
tembl-id:ECLACY   ECLACY        1500    1500    0       0       336     0
1164    77.599998       1.000000        E. coli lacY gene (codes for lactose pe
rmease).
tembl-id:ECLACZ   ECLACZ        3078    3078    0       0       373     0
2705    87.881744       1.000000        E. coli gene lacZ coding for beta-galac
tosidase (EC 3.2.1.23).

  Output files for usage example 9

  File: test.out

# USA             Name        SeqLen    AlignLen        Gaps    GapLen  Ident
Similar Differ  % Change        Weight  Description
tembl-id:ECLACZ   ECLACZ        3078    3078    0       0       3078    0
0       0.000000        1.000000        E. coli gene lacZ coding for beta-galac
tosidase (EC 3.2.1.23).

   The first non-blank line is the heading. This is followed by one line
   per sequence containing the following columns of data separated by one
   of more space or TAB characters:

     * The USA (Uniform Sequence Address) that EMBOSS can use to read in
       the sequence.
     * Name - name of the sequence.
     * SeqLen - length of the sequence when all gap characters are
       removed.
     * AlignLen - length of the sequence including internal gap
       characters i.e. gaps at the start or the end are not included.
     * Gaps - number of gaps e.g. 'AAA---AAA' is 1 gap (and 3 gap
       characters long (see GapLen)).
     * GapLen - total number of internal gap characters, see the 3 gap
       characters above. This is the sum total of all of the internal gap
       characters in this sequence.
     * Ident - number of characters that are identical to the specified
       reference sequence (uppercase 'A' is identical to lowercase 'a').
     * Similar - number of characters which are non-identical - which
       score > 0 in the comparison matrix when compared to the reference
       sequence, but which are not identical.
     * Different - number of characters which score <= 0 in the
       comparison matrix when compared to the reference sequence.
     * %Change - a simple measure of the percentage change as compared to
       the reference sequence: (AlignLen - Ident) * 100 / AlignLen
     * Description - the description annotation of the sequence (if any).

   If qualifiers to inhibit various columns of information are used, then
   the remaining columns of information are output in the same order as
   shown above, so if '-noseqlength' is used, the order of output is:
   usa, name, alignlength, gaps, gapcount, idcount, simcount, diffcount,
   change, description.

   When the -html qualifier is specified, then the output will be wrapped
   in HTML tags, ready for inclusion in a Web page. Note that tags such
   as
   and are not output by this program as the table of databases is
   expected to form only part of the contents of a web page - the rest of
   the web page must be supplier by the user.

   The lines of output information are guaranteed not to have trailing
   white-space at the end.

Data files

   infoalign reads in scoring matrices to determine the consensus
   sequence and to determine which matches are similar or not.

   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by the EMBOSS
   environment variable EMBOSS_DATA.

   To see the available EMBOSS data files, run:

% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".

   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

Notes

   By default, the output file starts each line with the USA of the
   sequence being described, so the output file is a list file that can
   be manually edited and read in by other EMBOSS programs using the
   list-file specification of '@filename'.

References

   None.

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 alignment program - interface to ClustalW program
   infoseq      Displays some simple information about sequences
   plotcon      Plot quality of conservation of a sequence alignment
   prettyplot   Displays aligned sequences, with colouring and boxing
   seealso      Finds programs sharing group names
   showalign    Displays a multiple sequence alignment
   showdb       Displays information on the currently available databases
   textsearch   Search sequence documentation. Slow, use SRS and Entrez!
   tfm          Displays a program's help documentation manual
   tranalign    Align nucleic coding regions given the aligned proteins
   whichdb      Search all databases for an entry
   wossname     Finds programs by keywords in their one-line documentation

Author(s)

   Gary Williams (gwilliam