MAKER version 3.1 and integration with resequencing

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MAKER version 3.1 and integration with resequencing

Ole Kristian Tørresen-2
Hi all,
I was asked to provide some text for a short description of assembly and annotation of a genome, and did some quick googling to see if I was up to date on what has happened with MAKER lately.

First I found the publication from last year describing sequencing and annotation of the desert woodrat (http://www.sciencedirect.com/science/article/pii/S2213596016300800). When reading that article, I saw references to MAKER 3.1. As far as I can see from http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi, the latest MAKER is 3.00.0-beta. Is 3.1 available somewhere, or is it going to be released soon?

I also saw that a poster that was presented at PAG last year (https://pag.confex.com/pag/xxiv/webprogram/Paper19035.html) and was intrigued with the last sentence “...integrating MAKER with resequencing efforts to enable rapid genotype-phenotype association.” Is this part of MAKER 3.1, or a separate effort? I am very interested in the status of this.

Thank you.

Sincerely,
Ole
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Re: MAKER version 3.1 and integration with resequencing

Carson Holt-2
Currently only 3.0 beta is available. It integrates EVM, and slightly alters some prediction hints for algorithms like Augustus.

It can be used to identify genes on a new reference or update existing gene models (requires that existing models be in GFF3 against the reference genome).

I think in the presentation Mark was referring to a separate MAKER fork.  The MAKER fork will take a species reference genome, a VCF file derived from resequenced individuals, and it will rebuild gene models around the individual variation. This allows us to identify simple changes like amino acid substitutions between individuals as well as complex changes related to splicing, exon skipping, etc.

It uses the prediction tool described in this paper (paper contains several examples of variation we can properly predict against) —> https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btw799/2736367/High-throughput-interpretation-of-gene-structure

—Carson



On Mar 9, 2017, at 2:36 AM, Ole Kristian Tørresen <[hidden email]> wrote:

Hi all,
I was asked to provide some text for a short description of assembly and annotation of a genome, and did some quick googling to see if I was up to date on what has happened with MAKER lately.

First I found the publication from last year describing sequencing and annotation of the desert woodrat (http://www.sciencedirect.com/science/article/pii/S2213596016300800). When reading that article, I saw references to MAKER 3.1. As far as I can see from http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi, the latest MAKER is 3.00.0-beta. Is 3.1 available somewhere, or is it going to be released soon?

I also saw that a poster that was presented at PAG last year (https://pag.confex.com/pag/xxiv/webprogram/Paper19035.html) and was intrigued with the last sentence “...integrating MAKER with resequencing efforts to enable rapid genotype-phenotype association.” Is this part of MAKER 3.1, or a separate effort? I am very interested in the status of this.

Thank you.

Sincerely,
Ole
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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Re: MAKER version 3.1 and integration with resequencing

Ole Kristian Tørresen-2
Hi Carson.

In the article I linked to, The draft genome sequence and annotation of the desert woodrat Neotoma lepida (http://www.sciencedirect.com/science/article/pii/S2213596016300800), this sentence is found: "To annotate the whole genome, MAKER version 3.1 was run on Neotoma lepida using Trinity assembled mRNA-seq reads (described above), and all annotated mouse and rat proteins available from NCBI (ftp://ftp.ncbi.nih.gov/genomes/).”

So I guess this version is not available, or maybe they meant 3.0beta1 or something.

ACE looks like a really cool tool, I’ll pass it on to people that have the correct datasets.

Thank you.

Ole

> On 09 Mar 2017, at 19:51, Carson Holt <[hidden email]> wrote:
>
> Currently only 3.0 beta is available. It integrates EVM, and slightly alters some prediction hints for algorithms like Augustus.
>
> It can be used to identify genes on a new reference or update existing gene models (requires that existing models be in GFF3 against the reference genome).
>
> I think in the presentation Mark was referring to a separate MAKER fork.  The MAKER fork will take a species reference genome, a VCF file derived from resequenced individuals, and it will rebuild gene models around the individual variation. This allows us to identify simple changes like amino acid substitutions between individuals as well as complex changes related to splicing, exon skipping, etc.
>
> It uses the prediction tool described in this paper (paper contains several examples of variation we can properly predict against) —> https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btw799/2736367/High-throughput-interpretation-of-gene-structure
>
> —Carson
>
>
>
>> On Mar 9, 2017, at 2:36 AM, Ole Kristian Tørresen <[hidden email]> wrote:
>>
>> Hi all,
>> I was asked to provide some text for a short description of assembly and annotation of a genome, and did some quick googling to see if I was up to date on what has happened with MAKER lately.
>>
>> First I found the publication from last year describing sequencing and annotation of the desert woodrat (http://www.sciencedirect.com/science/article/pii/S2213596016300800). When reading that article, I saw references to MAKER 3.1. As far as I can see from http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi, the latest MAKER is 3.00.0-beta. Is 3.1 available somewhere, or is it going to be released soon?
>>
>> I also saw that a poster that was presented at PAG last year (https://pag.confex.com/pag/xxiv/webprogram/Paper19035.html) and was intrigued with the last sentence “...integrating MAKER with resequencing efforts to enable rapid genotype-phenotype association.” Is this part of MAKER 3.1, or a separate effort? I am very interested in the status of this.
>>
>> Thank you.
>>
>> Sincerely,
>> Ole
>> _______________________________________________
>> maker-devel mailing list
>> [hidden email]
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>

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Re: MAKER version 3.1 and integration with resequencing

Carson Holt-2
My guess is that Michael may have called it 3.1 because he used the subversion repository which is beyond the 3.0-beta download but has not been packaged for release yet.

—Carson


> On Mar 9, 2017, at 12:42 PM, Ole Kristian Tørresen <[hidden email]> wrote:
>
> Hi Carson.
>
> In the article I linked to, The draft genome sequence and annotation of the desert woodrat Neotoma lepida (http://www.sciencedirect.com/science/article/pii/S2213596016300800), this sentence is found: "To annotate the whole genome, MAKER version 3.1 was run on Neotoma lepida using Trinity assembled mRNA-seq reads (described above), and all annotated mouse and rat proteins available from NCBI (ftp://ftp.ncbi.nih.gov/genomes/).”
>
> So I guess this version is not available, or maybe they meant 3.0beta1 or something.
>
> ACE looks like a really cool tool, I’ll pass it on to people that have the correct datasets.
>
> Thank you.
>
> Ole
>
>> On 09 Mar 2017, at 19:51, Carson Holt <[hidden email]> wrote:
>>
>> Currently only 3.0 beta is available. It integrates EVM, and slightly alters some prediction hints for algorithms like Augustus.
>>
>> It can be used to identify genes on a new reference or update existing gene models (requires that existing models be in GFF3 against the reference genome).
>>
>> I think in the presentation Mark was referring to a separate MAKER fork.  The MAKER fork will take a species reference genome, a VCF file derived from resequenced individuals, and it will rebuild gene models around the individual variation. This allows us to identify simple changes like amino acid substitutions between individuals as well as complex changes related to splicing, exon skipping, etc.
>>
>> It uses the prediction tool described in this paper (paper contains several examples of variation we can properly predict against) —> https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btw799/2736367/High-throughput-interpretation-of-gene-structure
>>
>> —Carson
>>
>>
>>
>>> On Mar 9, 2017, at 2:36 AM, Ole Kristian Tørresen <[hidden email]> wrote:
>>>
>>> Hi all,
>>> I was asked to provide some text for a short description of assembly and annotation of a genome, and did some quick googling to see if I was up to date on what has happened with MAKER lately.
>>>
>>> First I found the publication from last year describing sequencing and annotation of the desert woodrat (http://www.sciencedirect.com/science/article/pii/S2213596016300800). When reading that article, I saw references to MAKER 3.1. As far as I can see from http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi, the latest MAKER is 3.00.0-beta. Is 3.1 available somewhere, or is it going to be released soon?
>>>
>>> I also saw that a poster that was presented at PAG last year (https://pag.confex.com/pag/xxiv/webprogram/Paper19035.html) and was intrigued with the last sentence “...integrating MAKER with resequencing efforts to enable rapid genotype-phenotype association.” Is this part of MAKER 3.1, or a separate effort? I am very interested in the status of this.
>>>
>>> Thank you.
>>>
>>> Sincerely,
>>> Ole
>>> _______________________________________________
>>> maker-devel mailing list
>>> [hidden email]
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>


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Re: MAKER version 3.1 and integration with resequencing

Ole Kristian Tørresen-2
Ah, thank you. That explains it.

Ole

> On 09 Mar 2017, at 20:50, Carson Holt <[hidden email]> wrote:
>
> My guess is that Michael may have called it 3.1 because he used the subversion repository which is beyond the 3.0-beta download but has not been packaged for release yet.
>
> —Carson
>
>
>> On Mar 9, 2017, at 12:42 PM, Ole Kristian Tørresen <[hidden email]> wrote:
>>
>> Hi Carson.
>>
>> In the article I linked to, The draft genome sequence and annotation of the desert woodrat Neotoma lepida (http://www.sciencedirect.com/science/article/pii/S2213596016300800), this sentence is found: "To annotate the whole genome, MAKER version 3.1 was run on Neotoma lepida using Trinity assembled mRNA-seq reads (described above), and all annotated mouse and rat proteins available from NCBI (ftp://ftp.ncbi.nih.gov/genomes/).”
>>
>> So I guess this version is not available, or maybe they meant 3.0beta1 or something.
>>
>> ACE looks like a really cool tool, I’ll pass it on to people that have the correct datasets.
>>
>> Thank you.
>>
>> Ole
>>
>>> On 09 Mar 2017, at 19:51, Carson Holt <[hidden email]> wrote:
>>>
>>> Currently only 3.0 beta is available. It integrates EVM, and slightly alters some prediction hints for algorithms like Augustus.
>>>
>>> It can be used to identify genes on a new reference or update existing gene models (requires that existing models be in GFF3 against the reference genome).
>>>
>>> I think in the presentation Mark was referring to a separate MAKER fork.  The MAKER fork will take a species reference genome, a VCF file derived from resequenced individuals, and it will rebuild gene models around the individual variation. This allows us to identify simple changes like amino acid substitutions between individuals as well as complex changes related to splicing, exon skipping, etc.
>>>
>>> It uses the prediction tool described in this paper (paper contains several examples of variation we can properly predict against) —> https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btw799/2736367/High-throughput-interpretation-of-gene-structure
>>>
>>> —Carson
>>>
>>>
>>>
>>>> On Mar 9, 2017, at 2:36 AM, Ole Kristian Tørresen <[hidden email]> wrote:
>>>>
>>>> Hi all,
>>>> I was asked to provide some text for a short description of assembly and annotation of a genome, and did some quick googling to see if I was up to date on what has happened with MAKER lately.
>>>>
>>>> First I found the publication from last year describing sequencing and annotation of the desert woodrat (http://www.sciencedirect.com/science/article/pii/S2213596016300800). When reading that article, I saw references to MAKER 3.1. As far as I can see from http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi, the latest MAKER is 3.00.0-beta. Is 3.1 available somewhere, or is it going to be released soon?
>>>>
>>>> I also saw that a poster that was presented at PAG last year (https://pag.confex.com/pag/xxiv/webprogram/Paper19035.html) and was intrigued with the last sentence “...integrating MAKER with resequencing efforts to enable rapid genotype-phenotype association.” Is this part of MAKER 3.1, or a separate effort? I am very interested in the status of this.
>>>>
>>>> Thank you.
>>>>
>>>> Sincerely,
>>>> Ole
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> [hidden email]
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>
>

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Re: MAKER version 3.1 and integration with resequencing

Ole Kristian Tørresen-2
In reply to this post by Carson Holt-2
Ah, thank you. That explains it.

Ole

> On 09 Mar 2017, at 20:50, Carson Holt <[hidden email]> wrote:
>
> My guess is that Michael may have called it 3.1 because he used the subversion repository which is beyond the 3.0-beta download but has not been packaged for release yet.
>
> —Carson
>
>
>> On Mar 9, 2017, at 12:42 PM, Ole Kristian Tørresen <[hidden email]> wrote:
>>
>> Hi Carson.
>>
>> In the article I linked to, The draft genome sequence and annotation of the desert woodrat Neotoma lepida (http://www.sciencedirect.com/science/article/pii/S2213596016300800), this sentence is found: "To annotate the whole genome, MAKER version 3.1 was run on Neotoma lepida using Trinity assembled mRNA-seq reads (described above), and all annotated mouse and rat proteins available from NCBI (ftp://ftp.ncbi.nih.gov/genomes/).”
>>
>> So I guess this version is not available, or maybe they meant 3.0beta1 or something.
>>
>> ACE looks like a really cool tool, I’ll pass it on to people that have the correct datasets.
>>
>> Thank you.
>>
>> Ole
>>
>>> On 09 Mar 2017, at 19:51, Carson Holt <[hidden email]> wrote:
>>>
>>> Currently only 3.0 beta is available. It integrates EVM, and slightly alters some prediction hints for algorithms like Augustus.
>>>
>>> It can be used to identify genes on a new reference or update existing gene models (requires that existing models be in GFF3 against the reference genome).
>>>
>>> I think in the presentation Mark was referring to a separate MAKER fork.  The MAKER fork will take a species reference genome, a VCF file derived from resequenced individuals, and it will rebuild gene models around the individual variation. This allows us to identify simple changes like amino acid substitutions between individuals as well as complex changes related to splicing, exon skipping, etc.
>>>
>>> It uses the prediction tool described in this paper (paper contains several examples of variation we can properly predict against) —> https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btw799/2736367/High-throughput-interpretation-of-gene-structure
>>>
>>> —Carson
>>>
>>>
>>>
>>>> On Mar 9, 2017, at 2:36 AM, Ole Kristian Tørresen <[hidden email]> wrote:
>>>>
>>>> Hi all,
>>>> I was asked to provide some text for a short description of assembly and annotation of a genome, and did some quick googling to see if I was up to date on what has happened with MAKER lately.
>>>>
>>>> First I found the publication from last year describing sequencing and annotation of the desert woodrat (http://www.sciencedirect.com/science/article/pii/S2213596016300800). When reading that article, I saw references to MAKER 3.1. As far as I can see from http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi, the latest MAKER is 3.00.0-beta. Is 3.1 available somewhere, or is it going to be released soon?
>>>>
>>>> I also saw that a poster that was presented at PAG last year (https://pag.confex.com/pag/xxiv/webprogram/Paper19035.html) and was intrigued with the last sentence “...integrating MAKER with resequencing efforts to enable rapid genotype-phenotype association.” Is this part of MAKER 3.1, or a separate effort? I am very interested in the status of this.
>>>>
>>>> Thank you.
>>>>
>>>> Sincerely,
>>>> Ole
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> [hidden email]
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>
>

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