ALIFMT(1)

NAME

alifmt - Aligned sequences formats

DESCRIPTION
This document illustrates some common formats used for aligned sequences representation.

CLUSTAL
     CLUSTAL W (1.82) multiple sequence alignment

     MALK_ECOLI      MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTL
     MALK_SALTY      MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTL
     MALK_ENTAE      MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTL
     MALK_PHOLU      MSSVTLRNVSKAYGETIISKNINLEIQEGEF--------------
                     *:** *:**:**:*:.::**:***:*::***

     MALK_ECOLI      LRMIAGLETITSGDLACRRLHKEPGV
     MALK_SALTY      LRMIAGLETITSGDLACRRLHQEPGV
     MALK_ENTAE      LRMIAGLETVTSGDL-----------
     MALK_PHOLU      LRM-----------------------
                     ***

    Warning: Names must not contain spaces or exceed 30 characters.

FASTA
     >MALK_ECOLI
     MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
     GLETITSGDLACRRLHKEPGV
     >MALK_SALTY
     MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
     GLETITSGDLACRRLHQEPGV
     >MALK_ENTAE
     MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
     GLETVTSGDL-----------
     >MALK_PHOLU
     MSSVTLRNVSKAYGETIISKNINLEIQEGEF--------------LRM--
     ---------------------

MEGA
     #mega
     !Title Multiple Sequence Alignment;

     #MALK_ECOLI
     MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
     GLETITSGDLACRRLHKEPGV
     #MALK_SALTY
     MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
     GLETITSGDLACRRLHQEPGV
     #MALK_ENTAE
     MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
     GLETVTSGDL-----------
     #MALK_PHOLU
     MSSVTLRNVSKAYGETIISKNINLEIQEGEF-------------------
     ---------------------

MSF
     !!AA_MULTIPLE_ALIGNMENT 1.0
     PileUp of: @pep.list

      msf.seq       MSF: 55  Type: P  Nov 22, 2001 11:02  Check: 2529 ..

      Name: m73237           Len:   655  Check: 7493  Weight:  1.00
      Name: l28824           Len:   655  Check: 5456  Weight:  1.00
      Name: u04379           Len:   655  Check: 9580  Weight:  1.00

     //

             1                                                   50
     m73237  ~~~~~MADSA NHLPFFFGQI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG
     l28824  MASSGMADSA NHLPFFFGNI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG
     u04379  ~~~~~MPDPA AHLPFFYGSI SRAEAEEHLK LAGMADGLFL LRQCLRSLGG

             51
     m73237  ~~~~~
     l28824  ~~~~~
     u04379  AACG*

    Warning: This format cannot handle more than 500 sequences in a single alignment.

NEXUS
     #NEXUS

     begin data;
       dimensions ntax=2 nchar=80;
       format datatype=Protein interleave gap=- missing='.';
       matrix
     [           1                                               50]
     btdDm       -------AQQQQHHLHMQQAQHH-----------LHLSH------QQAQQ
     TSp1        --------------------AEH-----------PSLR--------GTPL

     [           51                          80]
     btdDm       YACPICSKKFSRSDHLSKHKKTHF------
     TSp1        FACPICNKRFMRSDHLAKHVKTHN------

         ;
     endblock;

    Warning: Text enclosed in brackets is considered as comment, and thus ignored.

PHYLIP
    Sequential (PHYLIPS):

          2   109
     ATISA1    GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENNDG
               ENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMGDE
               YGHTKGGN---
     POTISA1   GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKDG
               ENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMGDE
               YGHTKGGN---

    Interleaved (PHYLIPI):

          2   109
     ATISA1    GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENND
     POTISA1   GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKD

               GENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMG
               GENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMG

               DEYGHTKGGN---
               DEYGHTKGGN---

    Warning: Species names may not contain characters `( ) : ; , [ ]' and exceed 10 characters.

STOCKHOLM
     # STOCKHOLM 1.0

     MALK_ECOLI  MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
     MALK_SALTY  MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
     MALK_ENTAE  MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
     MALK_PHOLU  MSSVTLRNVSKAYGETIISKNINLEIQEGEF-------------------

     MALK_ECOLI  RCHLFREDGTACRRLHKEPGV
     MALK_SALTY  RCHLFREDGSACRRLHQEPGV
     MALK_ENTAE  ---------------------
     MALK_PHOLU  ---------------------
     //

SEE ALSO

squizz(1), seqfmt(5)

AUTHOR
Nicolas Joly (njoly@pasteur.fr), Institut Pasteur.