---
name: "est2genome"
section: "1e"
platform: "linux"
package: "emboss"
version: "6.6.0+dfsg-15"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/est2genome"
---

# est2genome(1e)

Align EST sequences to genomic DNA sequence

## NAME

est2genome - Align EST sequences to genomic DNA sequence

## SYNOPSIS

**est2genome** **-estsequence** *seqall* **-genomesequence** *sequence* \[**-match** *integer*\] \[**-mismatch** *integer*\] \[**-gappenalty** *integer*\] \[**-intronpenalty** *integer*\] \[**-splicepenalty** *integer*\] \[**-minscore** *integer*\] **-reverse** *boolean* **-usesplice** *boolean* **-mode** *list* **-best** *boolean* **-space** *float* **-shuffle** *integer* **-seed** *integer* **-outfile** *outfile* **-align** *boolean* **-width** *integer*

**est2genome** **-help**

## DESCRIPTION

**est2genome** is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Alignment:Global" command group(s).

## OPTIONS

### Input section

- **-estsequence** *seqall*

  - **-genomesequence** *sequence*

  ### Additional section

- **-match** *integer*

  Default value: 1

- **-mismatch** *integer*

  Default value: 1

- **-gappenalty** *integer*

  Cost for deleting a single base in either sequence, excluding introns Default value: 2

- **-intronpenalty** *integer*

  Cost for an intron, independent of length. Default value: 40

- **-splicepenalty** *integer*

  Cost for an intron, independent of length and starting/ending on donor-acceptor sites Default value: 20

- **-minscore** *integer*

  Exclude alignments with scores below this threshold score. Default value: 30

### Advanced section

- **-reverse** *boolean*

  Reverse the orientation of the EST sequence

- **-usesplice** *boolean*

  Use donor and acceptor splice sites. If you want to ignore donor-acceptor sites then set this to be false. Default value: Y

- **-mode** *list*

  This determines the comparison mode. The default value is 'both', in which case both strands of the est are compared assuming a forward gene direction (ie GT/AG splice sites), and the best comparison redone assuming a reversed (CT/AC) gene splicing direction. The other allowed modes are 'forward', when just the forward strand is searched, and 'reverse', ditto for the reverse strand. Default value: both

- **-best** *boolean*

  You can print out all comparisons instead of just the best one by setting this to be false. Default value: Y

- **-space** *float*

  For linear-space recursion. If product of sequence lengths divided by 4 exceeds this then a divide-and-conquer strategy is used to control the memory requirements. In this way very long sequences can be aligned. If you have a machine with plenty of memory you can raise this parameter (but do not exceed the machine's physical RAM) Default value: 10.0

- **-shuffle** *integer*

  - **-seed** *integer*

  Default value: 20825

### Output section

- **-outfile** *outfile*

  - **-align** *boolean*

  Show the alignment. The alignment includes the first and last 5 bases of each intron, together with the intron width. The direction of splicing is indicated by angle brackets (forward or reverse) or ???? (unknown).

- **-width** *integer*

  Default value: 50

## BUGS

Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group\_id=93650&atid=605031).

## SEE ALSO

est2genome is fully documented via the **tfm**(1) system.

## AUTHOR

**Debian Med Packaging Team** \<debian-med-packaging@lists.alioth.debian.org\>

Wrote the script used to autogenerate this manual page.

## COPYRIGHT

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.