---
name: "psa2msa"
section: "1"
platform: "linux"
package: "pftools"
version: "3.2.12-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/psa2msa"
---

# psa2msa(1)

reformat PSA file to Pearson/Fasta multiple sequence alignment file

## NAME

psa2msa -  reformat PSA file to Pearson/Fasta multiple sequence alignment file

## SYNOPSIS

- **psa2msa**

  \[ **-dhlpu** \] \[ **-M** *insert\_len* \] \[ **-W** *width* \] \[ *psa\_file* \| **-** \] \[ *parameters* \]

## DESCRIPTION

**psa2msa** reformats a [**psa**(5)](/psa/5.md) formatted profile-sequence alignment file into a Pearson/Fasta-formatted multiple sequence alignment file. The result is written to the standard output.  '*psa\_file*' contains alignments of several sequence segments to the same profile  in [**psa**(5)](/psa/5.md) format. Such a file is typically generated by the programs [**pfsearch**(1)](/pfsearch/1.md) or [**pfscan**(1)](/pfscan/1.md) using option **-x**. The output can be converted into other formats (*e.g.* MSF) with the aid of the public domain program **readseq** (available from *ftp://ftp.bio.indiana.edu/molbio/readseq*) or used directly with [**pfmake**(1)](/pfmake/1.md) or [**pfw**(1)](/pfw/1.md). If '**-**' is specified instead of a filename, the [**psa**(5)](/psa/5.md) alignment is read from the standard input.

## OPTIONS

- *psa\_file*

  Input multiple sequence alignment.\
   The content of the file must be in [**psa**(5)](/psa/5.md) format. If the filename is replaced by a '**-**', **psa2msa** will read the input alignment from **stdin**.

- **-d**

  Replace periods '**.**' by dashes '**-**' on output.

- **-h**

  Display usage help text.

- **-l**

  Replace upper case letters by lower case letters on output.

- **-p**

  Replace dashes '**-**' by periods '**.**' on output.

- **-u**

  Replace lower case letters by upper case letters on output.

- **-M** *insert\_len*

  Maximal length of an insertion.\
   If the real length of an insertion exceeds this value, the excess number  of residues will be deleted from the center of the insertion.  A negative value of '*insert\_len*' means no upper limit for the length of an insertion (*i.e.* no residues will be deleted from an insertion). If  '*insert\_len*' is zero, all insert positions will be removed. Setting an insertion length limit helps to keep the resulting alignment at manageable size.\
   Type: integer\
   Default: -1

  - Note:

    The meaning of the value '*0*' for this parameter has been changed compared to version 2.2 of the **pftools** package.

- **-W** *width*

  Set alignment output width.\
   The value of '*width*' specifies how many residues will be output on one line.\
   Type: integer\
   Default: 60

## PARAMETERS

- Note:

  for backwards compatibility, release 2.3 of the **pftools** package will parse the version 2.2 style parameters, but these are *deprecated* and the corresponding option (refer to the *options* section) should be used instead.

- M=#

  Maximal insertion length\
   Use option **-M** instead.

- W=#

  Output width.\
   Use option **-W** instead.

## EXAMPLES

- (1)

  **pfsearch** -bx ecp.prf CVPBR322 \|  **psa2msa** -du \| **readseq** -p -fMSF \> ecp.msf

-

  Generates a multiple sequence alignment of predicted *E. coli* promoters on both strands of plasmid pBR322. The file '*ecp.prf*' contains a profile for  *E. coli* promoters.   The file '*CVPBR322*' contains EMBL entry J01749\|CVPBR322. The result in '*ecp.msf*' can further be processed by GCG programs accepting MSF files as input.

## EXIT CODE

On successful completion of its task, **psa2msa** will return an exit code of 0. If an error occurs, a diagnostic message will be output on standard error and the exit code will be different from 0. When conflicting options where passed to the program but the task could nevertheless be completed, warnings will be issued on standard error.

## SEE ALSO

[**pfscan**(1)](/pfscan/1.md), [**pfsearch**(1)](/pfsearch/1.md), [**pfmake**(1)](/pfmake/1.md), [**pfw**(1)](/pfw/1.md), [**psa**(5)](/psa/5.md), [**xpsa**(5)](/xpsa/5.md)

## AUTHOR

The **pftools** package was developed by Philipp Bucher.\
 Any comments or suggestions should be addressed to \<pftools@sib.swiss\>.