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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">I recently tried msatfinder in bio-linux7 to compare it to misa that a colleague used. Msatfinder seemed to find all the same microsatellite sequences but on my system completely
failed to produce primers with the message "No valid primers found for ..." printed to the terminal. I know there are valid primers because misa found them (but I don't know what versions of things) and when I took the fasta sequence from the msatfinder FASTA
output folder, web based primer3 found several primer pairs.<br>
<br>
To troubleshoot I took a random sequence from human chr1<br>
(<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_000001.10?report=fasta&from=3556583&to=3665309" target="_blank">http://www.ncbi.nlm.nih.gov/nuccore/NC_000001.10?report=fasta&from=3556583&to=3665309</a>) and ran msatfinder on it.<br>
<br>
Here is the final microsat results from the terminal dump:<br>
Found (taaa)5 msat at 104492:<br>
FT repeat_region 104492..104511<br>
FT /label={taaa}5<br>
FT /note="(taaa)5"<br>
FT /note="Coding: 0"<br>
FT /note="Gene: N/A"<br>
FT /note="Product: N/A"<br>
FT /note="Protein: N/A"<br>
Opening output file 224589800_3556583-3665309.msat_tab<br>
Writing MINE file 224589800_3556583-3665309.104492.taaa.5.db<br>
Opening fasta FILE Fasta/224589800_3556583-3665309.104492.taaa.5.fasta<br>
Determining PCR primers.<br>
Outfile: Primers/224589800_3556583-3665309.104492.taaa.5.primers.txt<br>
Running command: /usr/bin/eprimer3 -sequence Primers/224589800_3556583-3665309.104492.taaa.5.temp -outfile Primers/224589800_3556583-3665309.104492.taaa.5.primers.txt -target 298,320 -primer<br>
Unlinking file: Primers/224589800_3556583-3665309.104492.taaa.5.temp<br>
No valid primers found for 224589800_3556583-3665309<br>
-----<br>
<br>
<br>
A total of 1 files surveyed<br>
Hs_chr_1_3556583-3665309<br>
Msatfinder finished!<br>
<br>
When I then went to the FASTA file (224589800_3556583-3665309.104492.taaa.5.fasta) primer3 on the web gave primers.
<br>
<br>
I turned on debugging info in the msatfinder.rc file which caused the temp file in the primers folder to not get deleted, running eprimer3 with that file gives this error:<br>
<br>
Error: Missing SEQUENCE tag<br>
<br>
Anyone know what the problem is?<br>
<br>
Cheers<br>
Jeremy<br>
<br>
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<div style="margin:0"><font size="3" face="Times New Roman,serif"><span style="font-size:12pt"><font size="2" color="#1F497D" face="Arial,sans-serif"><span style="font-size:10pt" lang="en-AU">Jeremy Shearman, PhD</span></font></span></font></div>
<div style="margin:0"><font size="3" face="Times New Roman,serif"><span style="font-size:12pt"><font size="4" color="#1F497D" face="Angsana New,serif"><span style="font-size:16pt" lang="th">เจเรอมี่</span></font><font size="4" color="#1F497D" face="Angsana New,serif"><span style="font-size:16pt" lang="th">
</span></font><font size="4" color="#1F497D" face="Angsana New,serif"><span style="font-size:16pt" lang="th">เชียร์แมน</span></font></span></font></div>
<div style="margin:0"><font size="3" face="Times New Roman,serif"><span style="font-size:12pt"><font size="2" color="#1F497D" face="Arial,sans-serif"><span style="font-size:10pt" lang="en-AU">National Centre for Genetic Engineering and Biotechnology, NSTDA</span></font><font size="2" color="#1F497D" face="Arial,sans-serif"><span style="font-size:10pt" lang="en-AU"><br>
113 Thailand Science Park, Phahonyothin Road, Klong1, Klong Luang, Pathumthani 12120</span></font></span></font></div>
<div style="margin:0"><font size="3" face="Times New Roman,serif"><span style="font-size:12pt"><font size="2" color="#1F497D" face="Arial,sans-serif"><span style="font-size:10pt" lang="en-AU">Ph: +66 2564 6700 ext. 3234 fax: +66 2564 6584</span></font></span></font></div>
<div style="margin:0"><font size="3" face="Times New Roman,serif"><span style="font-size:12pt"><font size="2" color="#1F497D" face="Calibri,sans-serif"><span style="font-size:11pt" lang="en-AU"> </span></font></span></font></div>
<div style="margin:0"><font size="3" face="Times New Roman,serif"><span style="font-size:12pt"><font size="2" color="#1F497D" face="Arial,sans-serif"><span style="font-size:10pt" lang="en-AU">ReasearcherID: F-1618-2010</span></font></span></font></div>
<div style="margin:0"><font size="3" face="Times New Roman,serif"><span style="font-size:12pt"><a href="http://www.researcherid.com/rid/F-1618-2010" target="_blank"><font size="2" face="Arial,sans-serif"><span style="font-size:10pt" lang="en-AU">http://www.researcherid.com/rid/F-1618-2010</span></font></a></span></font></div>
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