Hmm, 32 base pair translated sequences is pushing the envelope on blat
a little, but it could work!
On Mar 10, 2010, at 5:19 PM, Galt Barber wrote:
>
> Jim Kent informs me that you can do it this way:
>
> For the command line you can achieve this just by swapping target and
> query.
>
> Your 32bp sequences would become tiny targets,
> you would need -t=dnax -q=prot.
>
> Happy BLAT-TING!
>
> -Galt
>
> Galt Barber wrote:
>> Hi, Fabio!
>>
>> Here are the type combinations supported by blat from blat.c:
>>
>> if (bothSimpleNuc || bothSimpleProt)
>> {
>> [...]
>> }
>> else if (tType == gftDnaX && qType == gftProt)
>> {
>> [...]
>> }
>> else if (tType == gftDnaX && (qType == gftDnaX || qType == gftRnaX))
>> {
>> [...]
>> }
>> else
>> {
>> errAbort("Unrecognized combination of target and query types\n");
>>
>>
>>
>> What you would love to see and what is missing is this line:
>>
>> else if (tType == gftProt && (qType == gftDnaX || qType == gftRnaX))
>> {
>> [...]
>> }
>> But this combination is not supported by BLAT.
>> Perhaps Jim Kent felt that BLAST already did this well enough
>> and did not choose to support this.
>>
>> You could try converting your reads into 3 frames of protein
>> and then using blat -prot.
>>
>> By the way, if you are specifying -out-blast8 then you wouldn't
>> typically give your output file name the extension .psl.
>>
>> The results you got when using -prot on a dna query
>> are invalid. Do not use them.
>>
>> -Galt
>>
>> Fabio Gori wrote:
>>> Hi,
>>>
>>> Sice my reads are just 32bp long, I am trying to use blat instead
>>> of blastx to
>>> map them into proteins.
>>> I am trying to run
>>> blat nr.fa seqsaglobus.fa ris2.psl -t=prot -q=dnax -tileSize=8 -
>>> stepSize=3 -
>>> fine -repMatch=1000000 -out=blast8
>>>
>>> But I got the message:
>>> d and q must both be either protein or dna
>>>
>>> I tried with
>>> -t=prot -q=prot
>>> and I get some results, but it should not work because
>>> seqsaglobus.fa is made
>>> by nucleotides.
>>>
>>> Can you explain me what happens?
>>>
>>> Thank you,
>>>
>>> Fabio
>>>
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> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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