alifmt

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=89;
        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  ---------------------
      //