I have question about rice gene locus and RefSeq data
Gregory S. Brown
gregb at biotiquesystems.com
Mon Sep 18 09:21:55 EDT 2006
Hi,
The URL I posted for MartView was wrong. This is the correct url to
start with:
http://www.gramene.org/Multi/martview
The short explanation for the error is that I forgot to create the
correct bookmarkable url for the Mart page I sent you. At the
bottom of every Mart page is a way to create a URL that you save, put
into reports or send to people. For example the extremely long url
below is an example where the gene locus LOC_Os01g01340 is the target
of the Mart query. After clicking on the url below you can then
select whatever output options for external xref IDs that you would
like to see for this one locus and all of its transcripts. Hope this
helps and sorry for the initial confusion.
http://www.gramene.org/Multi/martview/martview?
osativa_gene_ensembl_chromosome_name=1&osativa_gene_ensembl_chromosome_n
ame_last=1&osativa_gene_ensembl_start=1&osativa_gene_ensembl_end=1000000
0&osativa_gene_ensembl_id_list_filters_filter=with_gramene_genesdb&osati
va_gene_ensembl_id_list_filters=Only&osativa_gene_ensembl_collection_id_
list_limit=1&osativa_gene_ensembl_id_list_limit_filters=ensembl_gene_id&
osativa_gene_ensembl_id_list_limit_filters_list=LOC_Os01g01340&osativa_g
ene_ensembl_with_5utr=Only&osativa_gene_ensembl_with_3utr=Only&osativa_g
ene_ensembl_biotype=protein_coding&osativa_gene_ensembl_biotype_last=pro
tein_coding&osativa_gene_ensembl_source=genbank&osativa_gene_ensembl_sou
rce_last=genbank&osativa_gene_ensembl_status=KNOWN&osativa_gene_ensembl_
status_last=KNOWN&osativa_gene_ensembl_evidence_code=IEA&osativa_gene_en
sembl_evidence_code_last=IEA&osativa_gene_ensembl_evidence_code_biol_pro
cess=IEA&osativa_gene_ensembl_evidence_code_biol_process_last=IEA&osativ
a_gene_ensembl_evidence_code_cell_component=IEA&osativa_gene_ensembl_evi
dence_code_cell_component_last=IEA&osativa_gene_ensembl_homolog_filters_
filter=osativa_paralog_bool&osativa_gene_ensembl_homolog_filters=Only&os
ativa_gene_ensembl_protein_fam_id_bools_filter=with_profile&osativa_gene
_ensembl_protein_fam_id_bools=Only&osativa_gene_ensembl_snptype_filters_
filter=with_coding_snp&osativa_gene_ensembl_snptype_filters=Only&osativa
_gene_ensembl_syn_status_filter=with_synonymous_snp&osativa_gene_ensembl
_syn_status=Only&osativa_gene_ensembl_with_validated_snp=Only&default_li
nk=---&default_link_last=---
&stage=output&osativa_gene_ensembl_id_list_filters_last=Only&schema=defa
ult&collection_seq_scope_type=transcript_exon_intron&osativa_gene_ensemb
l_with_5utr_last=Only&osativa_gene_ensembl_homolog_filters_last=Only&dat
aset_last=osativa_gene_ensembl&osativa_gene_ensembl_with_3utr_last=Only&
stage_initialised=start&stage_initialised=filter&outformat=html&stage_pr
ev=output&seq_scope=tscr&schema_last=default&osativa_gene_ensembl_syn_st
atus_last=Only&osativa_gene_ensembl_start_last=1&osativa_gene_ensembl_en
d_last=10000000&outcompress=none&osativa_gene_ensembl_protein_fam_id_boo
ls_last=Only&dataset=osativa_gene_ensembl&status_count_start=57752&datab
ase=Ensembl39__default&osativa_gene_ensembl_with_validated_snp_last=Only
&database_last=Ensembl39__default&osativa_gene_ensembl_snptype_filters_l
ast=Only&outtype=feature_page&collection_ensembl_attributes=ensembl_gene
_id&collection_ensembl_attributes=ensembl_transcript_id&collection_prot_
domain_this=prints&collection_chromosome_attributes=str_chrom_name&colle
ction_ensembl_attributes_structure=gene_stable_id&collection_ensembl_att
ributes_structure=biotype&collection_seq_scope_type_this=osativa_genomic
_sequence.gene_exon_intron&collection_gene=str_chrom_name&collection_gen
e=gene_stable_id&collection_transcript=biotype&osativa_gene_ensembl_id_l
ist_limit_filters_last=ensembl_gene_id&osativa_gene_ensembl_protein_fam_
id_filters_last=interpro&status_count_filter=1
gb
Greg Brown
On Sep 17, 2006, at 8:59 PM, Wenchi Chang_NTHU wrote:
> Dear Greg,
> Thank you very much for your reply.
> I have connected to the http://www.gramene.org/Multi/martview.
> The web message always reply "proxy error" (like atteched file).
> However,the other pages in http://www.gramene.org are working, but
> "/multi/martview".
> I have also used different computers to try, but also response the
> same error message.
> Are there any setting I should set on my computer?
> Could you please reply me?
> Thank you very much!
>
> Best Regards,
>
> Chang, wenchi
>
>
>
>
>
> ----- Original Message ----- From: "Gregory S. Brown"
> <gregb at biotiquesystems.com>
> To: <gramene at gramene.org>; "Wenchi Chang_NTHU"
> <d928204 at oz.nthu.edu.tw>
> Sent: Saturday, September 16, 2006 4:52 AM
> Subject: Re: I have question about rice gene locus and RefSeq data
>
>
>> Hi,
>>
>> If I understand your question correctly, you want a listing of a
>> Genbank peptide accession id that is associated with a given
>> Gramene gene locus id, i.e;
>> Gramene gene ID RefSeq peptide
>> -----------------------------------
>> LOC_Os01g01340 XP_549822
>>
>> The easiest way to get this information is by using the Gramene
>> Multi MartView system via the web interface. http://
>> www.gramene.org/Multi/ martview/qVTCczlV4p.mart
>>
>> Select the correct genome on this first page (Rice Gene Models
>> (TIGRv4)). The second page lets you restrict the search in many
>> ways. One way to accomplish your goal is to enter one or more
>> Gramene IDs in the "ID list limit" box. On the next page are
>> options for the output. This page will let you select "RefSeq
>> Peptide ID" and/or "RefSeq Peptide Predicted ID". Select the
>> type of output you need and then hit the export button.
>>
>> There is a pretty good help page for Mart here that will help you
>> navigate this very powerful system: http://www.gramene.org/
>> Oryza_sativa/helpview?se=1;ref=http%3A%2F%2Fwww.gramene.org%
>> 2Fdocumentation%2F;kw=martview
>>
>> There should be a direct link to MartView from each Gramene Gene
>> Report page. Apparently there is a small bug in the current
>> release as I do not see the link to "Export Gene info in region"
>> in the left navigation menu.
>>
>> Hope this helps. Good luck!
>>
>> Greg Brown
>>
>>
>>
>>
>> On Sep 14, 2006, at 9:37 PM, Wenchi Chang_NTHU wrote:
>>
>>> Dear Sir,
>>> Excuse me to trouble you.
>>> I'm a PhD student in Taiwan.
>>> Your database is so powerful and useful.
>>> However, I want to know how to download the corresponding locus
>>> ID and GenBank accession number (RefSeq peptide predicted on
>>> your website)of a gene?
>>> For example, LOC_Os01g01340 V.S. RefSeq peptide predicted
>>> XP_549822.1 ( http://www.gramene.org/Oryza_sativa/geneview?
>>> gene=LOC_Os01g01340)
>>> Could you please help and reply me.
>>> Because I found this kind of data over many many databses, but
>>> only supplied on your website.
>>> If you could reply me, I would be very very happy.
>>> Thank you very much!
>>>
>>> Best Regards,
>>>
>>> Chang, wenchi
>>>
>>> <004601c6d878$4de0efa0$1d0aa8c0>
>>>
>>>
>>
>>
>> <01.JPG>
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