How can I obtain seqences of M. incoginita?

[yoshi]

 Hi,

I carried out a BLAST search.

Then I obtained a sequence producing significant alignment below.

gn1 |MincDB| prot:Minc09124 length:471 contig:Miclctg314 region:48...
Score (bits) 531 E Value e-151

This is a protein sequence alignment.
I want a nucleotide sequence responsible for the protein sequence.

How can I obtain the nucleotide sequence?

[John Martin]

Hi Yoshi,
    You can download the sequence of that protein (Minc09124) using the NemaGene interface.   Goto this URL:

http://www.nematode.net/NN3_frontpage.cgi?navbar_selection=nemagene&subnav_selection=nemagene_new
 
(or navigate to the "NemaGene aearch" page  within the Nematode.net website).  Once there, open the "Filter Selection" area and enter "Minc09124" in the "Gene or Transcript name" field.   Then hit "Search NemaGene".

    The search may take a few seconds, but eventually it will display a page showing a long list of species results.   You will need to scroll down to the "Meloidogyne incognita" block in the long list to see your gene, you should see a link there to your protein sequence.   Click that link to jump to the detail page for that protein.  (Note that you can avoid the super-long list of species by selecting the specific species of interest in the "Species selection" area, then you will only be displayed blocks for the species you chose to look at)

    This final page will show you the various annotation we have for that protein, as well as the nucleotide and/or protein sequence (in the case of Minc09124 we only have protein sequence showing).   Immediately above the protein sequence you should see a link labeled "Download this sequence".   Click that and NemaGene will dump the sequence into a fasta file.   You'll be taken to yet another page with a link, right-click-save that link, which is your fasta file.

    One last note, you could also have generated that same fasta from the page with the long list of species blocks.   At the top of that list there is another "Download these sequences" link that will build you a fasta file of all the returned sequences in this intermediate list.   That link is more useful when you are defining a collection of sequences you'd like to download.   But in this case your filter resulted in only a single sequence, so it really doesn't matter if you go to the detail report page, or grab it here.

Thanks,
John Martin

[John Martin]

Ah, I just noticed that you are in fact asking for the nucleotide sequence for this protein.  Unfortunately in this case we only have the protein sequence in NemaGene.  The source of this entry is WormBase, so you might be able to find CDS if you search around in the WormBase FTP at:

ftp://ftp.wormbase.org/pub/wormbase/releases/WS238/species/m_incognita/PRJEA28837/

The data currently hosted in NemaGene is from WB release 238, but if they don't have the CDS in that release, you might try looking in more recent releases.   But be careful, if you use a different release you will need to double-check if you require CDS that matches perfectly to the protein that you hit in NemaBlast.

Thanks,
John Martin




On Wednesday, September 10, 2014 5:12:58 AM UTC-5, yoshi wrote:

[yoshi]

Hi John,

Thank you for your help.

According to your guidance, I could get to "right-click-save that link".

However, I could not see either "same fasta from the page with the long list of species blocks" or another "Download these sequences".

Could you please show me the URL of the final page describing the nucleotide sequence of Minc09124.


Sincerely,
Yoshi

[yoshi]

Hi John,

Thank you for your advise.
When I tried to connect the ftp server below, the server asked me user name (ID) and password.
How Can I obtain the user ID and the password from the server?
Please show me.

Sincerely,
Yoshi


2014年9月11日木曜日 8時26分30秒 UTC+9 John Martin:

[John Martin]

Yoshi,
    This URL should take you directly to the detail page for Minc09124:

http://www.nematode.net/NN3_frontpage.cgi?navbar_selection=nemagene&subnav_selection=detail_report_ext&name_for_detail_report_ext=Minc09124

Right above the protein sequence you should see a "Download this sequence" link.   You need to CLICK that link, which will cause the database to build the fasta for your selected protein.   Then you will end up at another page, this one will have a link with a name like:

Sequence.#####.faa

That link is the one you need to right-click -> save-link  to get the fasta.


Thanks,
John

[John Martin]

That is strange, I don't think you need a password to connect to that WormBase FTP.    Try using your internet browser, put the full path in as the URL:


ftp://ftp.wormbase.org/pub/wormbase/releases/WS238/species/m_incognita/PRJEA28837/

or you should be able to click it right here.   For me that takes me directly into the WormBase FTP site into the WS238 release for M.incognita.  I am not logged in, nor did it ask me for a password.

Note that if you are using command line sftp, that might ask you for a username & password.   If you prefer to use command line to goto that FTP, I think you can login anonymously:

user: anonymous
password: <use your email>

But its probably easiest if you just use the link in your browser.  

[yoshi]

Hi Martin,

I could obtain the whole genomic sequence of M. incognita from the WormBase FTP site into the WS238.

Thank you very much for your advise.

However, the sequence data is too large for my PC to treat. So, could not find the nucleotide sequence responsible for the protein  which I am interested in.

In the WormBase, I can easily find the cDNA and genomic sequences responsible for the C. elegans protein  which I am interested in.

As for M. incognita, it is so difficult to obtain nucleotide sequences in the limited region which I want.

Is there an EST database of M. incognita or a nucleotide database for CDS?

Sincerely,

Yoshi


2014年9月12日金曜日 8時00分32秒 UTC+9 John Martin:

[John Martin]

Yoshi,

    We do host M.incognita sanger EST contigs which are putatitive transcripts.   You can download a fasta of these M.inc. contigs using this link:

http://www.nematode.net/Data/cluster_ftp/SUMMARY/CLUSTER_SUMMARY.050621.meloidogyne_incognita

In order to correlate your protein(s) of interest to the sequence names in this fasta, you can use NemaBlast:

http://www.nematode.net/NN3_frontpage.cgi?navbar_selection=nemagene&subnav_selection=nemablast_vs_contigs

Just drop your protein sequence of interest into the search window, make sure to select M.incognita as a db, and make sure to set the blast type depending on your query sequence (use blastn if your query is nucleotide, tblastn if its protein).   The IDs used in the EST contigs file will match the subject IDs returned from the blast search.

John