{ "id": 418602, "title": "Information in the first line of each FASTA record in training_sequences.fasta", "url": "/competitions/cafa-5-protein-function-prediction/discussion/418602", "author_name": "", "post_date": "2023-06-21T14:21:54.187677300Z", "votes": 3, "comment_count": 3, "views": 0, "content": "

Hi all,

\n

I am trying to understand the information in the first line of the each FASTA record. Based on the data page:

\n
\n

For example, sp|P9WHI7|RECN_MYCT in the FASTA header indicates the protein with UniProt ID P9WHI7 and gene name RECN_MYCT was taken from Swiss-Prot (sp). Any sequences taken from TrEMBL will have tr in the header instead of sp

\n
\n

However looking at the actual fasta files the header line looks like:

\n
\n

>P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1
\n >O73864 sp|O73864|WNT11_DANRE Protein Wnt-11 OS=Danio rerio OX=7955 GN=wnt11 PE=2 SV=1

\n
\n

Is there any explanation for the rest of the data in this line?

", "messages": [ { "id": "2311908", "postDate": "06/21/2023 14:21:54", "content": "

Hi all,

\n

I am trying to understand the information in the first line of the each FASTA record. Based on the data page:

\n
\n

For example, sp|P9WHI7|RECN_MYCT in the FASTA header indicates the protein with UniProt ID P9WHI7 and gene name RECN_MYCT was taken from Swiss-Prot (sp). Any sequences taken from TrEMBL will have tr in the header instead of sp

\n
\n

However looking at the actual fasta files the header line looks like:

\n
\n

>P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1
\n >O73864 sp|O73864|WNT11_DANRE Protein Wnt-11 OS=Danio rerio OX=7955 GN=wnt11 PE=2 SV=1

\n
\n

Is there any explanation for the rest of the data in this line?

", "rawMarkdown": "Hi all,\n\nI am trying to understand the information in the first line of the each FASTA record. Based on the data page:\n\n>For example, sp|P9WHI7|RECN_MYCT in the FASTA header indicates the protein with UniProt ID P9WHI7 and gene name RECN_MYCT was taken from Swiss-Prot (sp). Any sequences taken from TrEMBL will have tr in the header instead of sp\n\nHowever looking at the actual fasta files the header line looks like:\n\n> \\>P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1\n> \\>O73864 sp|O73864|WNT11_DANRE Protein Wnt-11 OS=Danio rerio OX=7955 GN=wnt11 PE=2 SV=1\n\nIs there any explanation for the rest of the data in this line?", "votes": null }, { "id": "2312012", "postDate": "06/21/2023 15:41:52", "content": "

this may help: https://www.uniprot.org/help/fasta-headers

", "rawMarkdown": "this may help: https://www.uniprot.org/help/fasta-headers", "votes": null }, { "id": "2316415", "postDate": "06/24/2023 22:06:17", "content": "

Thank you!

\n

Is there an out-of-the-box parser that would parse the header row's metadata into something like a dictionary? I have been using Bio.SeqIO.FastaIO.FastaTwoLineParser however i don't think it parsers the additional information, just sets it in the description (which seems to be the entire header row)

", "rawMarkdown": "Thank you!\n\nIs there an out-of-the-box parser that would parse the header row's metadata into something like a dictionary? I have been using [Bio.SeqIO.FastaIO.FastaTwoLineParser](https://biopython.org/docs/1.75/api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineParser) however i don't think it parsers the additional information, just sets it in the description (which seems to be the entire header row)", "votes": null }, { "id": "2316562", "postDate": "06/25/2023 05:01:44", "content": "

Don't know actually, I generally go to the rute of creating a dictionary myself from the description of SeqIO

", "rawMarkdown": "Don't know actually, I generally go to the rute of creating a dictionary myself from the description of SeqIO", "votes": null } ], "comments": [ { "id": 2312012, "author_name": "mtinti", "author_url": "", "post_date": "06/21/2023 15:41:52", "content": "

this may help: https://www.uniprot.org/help/fasta-headers

", "votes": null, "replies": [ { "id": 2316415, "author_name": "h4ashbang", "author_url": "", "post_date": "06/24/2023 22:06:17", "content": "

Thank you!

\n

Is there an out-of-the-box parser that would parse the header row's metadata into something like a dictionary? I have been using Bio.SeqIO.FastaIO.FastaTwoLineParser however i don't think it parsers the additional information, just sets it in the description (which seems to be the entire header row)

", "votes": null, "replies": [ { "id": 2316562, "author_name": "mtinti", "author_url": "", "post_date": "06/25/2023 05:01:44", "content": "

Don't know actually, I generally go to the rute of creating a dictionary myself from the description of SeqIO

", "votes": null, "replies": [] } ] } ] } ], "raw_markdown_by_id": { "2311908": "Hi all,\n\nI am trying to understand the information in the first line of the each FASTA record. Based on the data page:\n\n>For example, sp|P9WHI7|RECN_MYCT in the FASTA header indicates the protein with UniProt ID P9WHI7 and gene name RECN_MYCT was taken from Swiss-Prot (sp). Any sequences taken from TrEMBL will have tr in the header instead of sp\n\nHowever looking at the actual fasta files the header line looks like:\n\n> \\>P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1\n> \\>O73864 sp|O73864|WNT11_DANRE Protein Wnt-11 OS=Danio rerio OX=7955 GN=wnt11 PE=2 SV=1\n\nIs there any explanation for the rest of the data in this line?", "2312012": "this may help: https://www.uniprot.org/help/fasta-headers", "2316415": "Thank you!\n\nIs there an out-of-the-box parser that would parse the header row's metadata into something like a dictionary? I have been using [Bio.SeqIO.FastaIO.FastaTwoLineParser](https://biopython.org/docs/1.75/api/Bio.SeqIO.FastaIO.html#Bio.SeqIO.FastaIO.FastaTwoLineParser) however i don't think it parsers the additional information, just sets it in the description (which seems to be the entire header row)", "2316562": "Don't know actually, I generally go to the rute of creating a dictionary myself from the description of SeqIO" }, "source": "meta" }