Append value in a file Post: 302253886

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alifmt

ALIFMT(5)							   User Manuals 							 ALIFMT(5)

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=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	---------------------
	    //

SEE ALSO

       squizz(1), seqfmt(5)

AUTHOR

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

Unix								    2009-05-19								 ALIFMT(5)

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gzip a file and append creation date stamp to file

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