Protein Alignment Simple Output Format

Question

[Maria]

Is there any web based service for global alignment whose output is simple i.e only the amino acids and the gaps without anything on margins before and after the 2 sequences for example:

MYIS
-NIS

I tried emboss and blast and couldn't figure out how to have such output. Thanks in advance

Answer 1

[Pierre Lindenbaum]

for BLAST, save the result as XML. And use the following XSLT stylesheet. It only prints the Hsp_qseq and the Hsp_hseq of the first hit and first hsp.

<xsl:stylesheet xmlns:xsl="&lt;a href=" <a="" href="http://www.w3.org/1999/XSL/Transform" rel="nofollow">http://www.w3.org/1999/XSL/Transform" "="" rel="nofollow">http://www.w3.org/1999/XSL/Transform' version='1.0' >
<xsl:output method="text"/>
<xsl:template match="/">
<xsl:apply-templates select="BlastOutput/BlastOutput_iterations/Iteration/Iteration_hits/Hit[1]/Hit_hsps/Hsp[1]"/>
</xsl:template>
<xsl:template match="Hsp">
<xsl:value-of select="Hsp_qseq"/><xsl:text>
</xsl:text><xsl:value-of select="Hsp_hseq"/><xsl:text>
</xsl:text>
</xsl:template>
</xsl:stylesheet>

.usage:

$ xsltproc --novalid stylesheet.xsl blast.xml

.

IDVWTEER-KGTLNRDLLFD
ID--TEERLKGVI--DLIFE

[Hamish]

BLAST (Basic Local Alignment Search Tool) does not perform a global alignment.

Answer 2

[arnstrm]

There are many multiple alignment programs and most of them use global alignment. Almost all of them output results (alignment) in more than one type (see types here). Just select the format you want and use the program of your choice to get your job done!

[Hamish]

For pairwise and multiple sequence alignment formats supported by EMBOSS see:

• 5.4.2. Supported Alignment Formats
• Appendix A. File Format Reference