tblastx is taking a sufficiently long time to run and is making my hopeful i may get some kind of actual output. no idea why blastn wouldnt be returning anything tho
November 27, 2025 at 10:27 PM
tblastx is taking a sufficiently long time to run and is making my hopeful i may get some kind of actual output. no idea why blastn wouldnt be returning anything tho
trying to run blastn from command line for a class project and i want to [ ]. i keep getting an empty file as my output lol
November 27, 2025 at 10:25 PM
trying to run blastn from command line for a class project and i want to [ ]. i keep getting an empty file as my output lol
sorry, it's late. how did you catch that from the BLASTn results alone?
November 27, 2025 at 1:11 PM
sorry, it's late. how did you catch that from the BLASTn results alone?
blastn took <10 seconds. ok there it is! smack in the BRCA2 mRNA sequence. as expected, only one of the nucleotide codes returned any BLAST hits at all
November 27, 2025 at 12:44 PM
blastn took <10 seconds. ok there it is! smack in the BRCA2 mRNA sequence. as expected, only one of the nucleotide codes returned any BLAST hits at all
MetaGraphを試してみたけど、全然使い方がわからない。試しにqueryやalignしてみたが、出力が理解不能。短い塩基配列検索でBLASTN代わりに使うようなケースには対応できないのだろうか？
November 13, 2025 at 7:02 PM
MetaGraphを試してみたけど、全然使い方がわからない。試しにqueryやalignしてみたが、出力が理解不能。短い塩基配列検索でBLASTN代わりに使うようなケースには対応できないのだろうか？
MetaGraphがNCBI ntでBLASTNの代わりになるかどうかテストしようとしているが、NCBI ntがでかいのでなかなか大変。FASTAの書き出しだけでもすごい時間かかる。
October 18, 2025 at 9:55 PM
MetaGraphがNCBI ntでBLASTNの代わりになるかどうかテストしようとしているが、NCBI ntがでかいのでなかなか大変。FASTAの書き出しだけでもすごい時間かかる。
メタゲノムを対象に検索してみたが、かなり類似度の低い配列も取ってこれるようだ。BLASTNの代わりになるか？代わりになるのだとしたら、あと1年早く出して欲しかったな…。いやGitHubには前からあったみたいなので、気付かなかった俺が悪いのか。BLAST DBに対応していれば助かるんだが、FASTA/FASTQしか対応していないようだ。NCBI ntのFASTAを用意しないといけないのか…。めんどくせーなー。
October 18, 2025 at 5:38 PM
メタゲノムを対象に検索してみたが、かなり類似度の低い配列も取ってこれるようだ。BLASTNの代わりになるか？代わりになるのだとしたら、あと1年早く出して欲しかったな…。いやGitHubには前からあったみたいなので、気付かなかった俺が悪いのか。BLAST DBに対応していれば助かるんだが、FASTA/FASTQしか対応していないようだ。NCBI ntのFASTAを用意しないといけないのか…。めんどくせーなー。
Authors published a paper in Biorxiv, they used BLASTN in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
www.biorxiv.org
October 16, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used BLASTN in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
🚀 Released gbdraw v0.6.0!
- Added dinucleotide skew plotting to linear mode. Fixed the bug where only GC skew could be drawn.
- Added links to relevant sections of the documentation throughout the web app help menu.
Try out:👉 gbdraw.streamlit.app
- Added dinucleotide skew plotting to linear mode. Fixed the bug where only GC skew could be drawn.
- Added links to relevant sections of the documentation throughout the web app help menu.
Try out:👉 gbdraw.streamlit.app
October 9, 2025 at 2:01 PM
🚀 Released gbdraw v0.6.0!
- Added dinucleotide skew plotting to linear mode. Fixed the bug where only GC skew could be drawn.
- Added links to relevant sections of the documentation throughout the web app help menu.
Try out:👉 gbdraw.streamlit.app
- Added dinucleotide skew plotting to linear mode. Fixed the bug where only GC skew could be drawn.
- Added links to relevant sections of the documentation throughout the web app help menu.
Try out:👉 gbdraw.streamlit.app
Authors published a paper in Biorxiv, they used BLASTN in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #OpenScience
www.biorxiv.org
October 8, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used BLASTN in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #OpenScience
DFAST (sorta PGAP fromthe DDBJ)
Not overly complicated to add custom annotation sources (blastn, blastp, rps-blast, hmm-based...)
Not overly complicated to add custom annotation sources (blastn, blastp, rps-blast, hmm-based...)
October 4, 2025 at 6:31 PM
DFAST (sorta PGAP fromthe DDBJ)
Not overly complicated to add custom annotation sources (blastn, blastp, rps-blast, hmm-based...)
Not overly complicated to add custom annotation sources (blastn, blastp, rps-blast, hmm-based...)
or a search can be restricted to only Drosophila melanogaster databases.
Once you enter a DNA or protein sequence in the search box, you'll be offered appropriate options for the nucleotide or protein databases you wish to search.
Once you enter a DNA or protein sequence in the search box, you'll be offered appropriate options for the nucleotide or protein databases you wish to search.
September 26, 2025 at 9:06 PM
or a search can be restricted to only Drosophila melanogaster databases.
Once you enter a DNA or protein sequence in the search box, you'll be offered appropriate options for the nucleotide or protein databases you wish to search.
Once you enter a DNA or protein sequence in the search box, you'll be offered appropriate options for the nucleotide or protein databases you wish to search.
Authors published a paper in Biorxiv, they used BLASTN in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #STMpublishing
www.biorxiv.org
September 5, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used BLASTN in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #STMpublishing
watched john wick 2 blastn thru all the movies this weeknd!
August 23, 2025 at 2:40 AM
watched john wick 2 blastn thru all the movies this weeknd!
Authors published a paper in Biorxiv, they used BLASTN in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #reproducibility
www.biorxiv.org
August 18, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used BLASTN in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #reproducibility
BLASTNを使われている皆さん、最もよく使うクエリの長さは以下のうちどれですか？
Hey, BLASTN users, which of these is the most common length for your queries?
100 bp or less
101–500 bp
501–1000 bp
1001–2000 bp
2001–5000 bp
5001 bp or more
Hey, BLASTN users, which of these is the most common length for your queries?
100 bp or less
101–500 bp
501–1000 bp
1001–2000 bp
2001–5000 bp
5001 bp or more
August 15, 2025 at 9:31 PM
BLASTNを使われている皆さん、最もよく使うクエリの長さは以下のうちどれですか？
Hey, BLASTN users, which of these is the most common length for your queries?
100 bp or less
101–500 bp
501–1000 bp
1001–2000 bp
2001–5000 bp
5001 bp or more
Hey, BLASTN users, which of these is the most common length for your queries?
100 bp or less
101–500 bp
501–1000 bp
1001–2000 bp
2001–5000 bp
5001 bp or more
Authors published a paper in Biorxiv, they used BLASTN in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #methodsmatter
www.biorxiv.org
August 13, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used BLASTN in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #methodsmatter
Authors published a paper in Biorxiv, they used BLASTN in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #reproducibility
www.biorxiv.org
August 5, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used BLASTN in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #reproducibility
GitHub Actionsのrunnerと、手元のローカルマシンでテストしたところ、BLAST+ 2.17.0ではバグが修正されているっぽい。BLAST+ 2.16.0のバグは、blastdb_aliastoolで複数のBLASTDBを束ねたaggregated BLASTDBを作成し、さらにそのaggregated BLASTDBのsubset BLASTDBを作成し、それに対してマルチスレッドでblastn検索するとフリーズすることがある、というもの。さきほどBLAST+ 2.17.0で50回そういうBLASTDBでマルチスレッドblastnを実行したが、全て問題なかった。
August 2, 2025 at 7:40 PM
GitHub Actionsのrunnerと、手元のローカルマシンでテストしたところ、BLAST+ 2.17.0ではバグが修正されているっぽい。BLAST+ 2.16.0のバグは、blastdb_aliastoolで複数のBLASTDBを束ねたaggregated BLASTDBを作成し、さらにそのaggregated BLASTDBのsubset BLASTDBを作成し、それに対してマルチスレッドでblastn検索するとフリーズすることがある、というもの。さきほどBLAST+ 2.17.0で50回そういうBLASTDBでマルチスレッドblastnを実行したが、全て問題なかった。
Es gibt verschiedene BLAST-Varianten. Man kann eine DNA-Sequenz als Query nutzen und damit in einer Datenbank aus DNA-Sequenzen suchen. Das ist dann BLASTn (n wie Nukleotid). Das Gleiche geht auch für Proteinsequenzen untereinander (BLASTp).
12/x
12/x
July 19, 2025 at 9:15 AM
Es gibt verschiedene BLAST-Varianten. Man kann eine DNA-Sequenz als Query nutzen und damit in einer Datenbank aus DNA-Sequenzen suchen. Das ist dann BLASTn (n wie Nukleotid). Das Gleiche geht auch für Proteinsequenzen untereinander (BLASTp).
12/x
12/x
Built a web app to visualize BLASTN/TBLASTX XML results as SVG dotplots. Try it out:
blast2dotplot.streamlit.app
blast2dotplot.streamlit.app
July 16, 2025 at 9:35 AM
Built a web app to visualize BLASTN/TBLASTX XML results as SVG dotplots. Try it out:
blast2dotplot.streamlit.app
blast2dotplot.streamlit.app
Authors published a paper in Biorxiv, they used BLASTN in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #OpenScience
Development of a Flex-Seq SNP panel for raspberry (Rubus idaeus L.) and validation through linkage map construction and identification of QTL for several traits of agronomic importance to raspberry breeding
www.biorxiv.org
July 13, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used BLASTN in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #OpenScience
これで実運用開始したらBLASTNより遅いじゃん、とかなったら泣ける。あり得るのがこえーんだよな。BLAST遅い遅い、メモリ使いすぎとユーザーとしては思っているが、開発者として見ると何気にデータベースもメモリ使用量もすごい小さいんですよね。NCBI ntはあれでものすごい小さくなってるんですよ。
July 2, 2025 at 3:44 AM
これで実運用開始したらBLASTNより遅いじゃん、とかなったら泣ける。あり得るのがこえーんだよな。BLAST遅い遅い、メモリ使いすぎとユーザーとしては思っているが、開発者として見ると何気にデータベースもメモリ使用量もすごい小さいんですよね。NCBI ntはあれでものすごい小さくなってるんですよ。
BLASTNに代わる塩基配列検索システムを開発している。Claude Codeのおかげでかなりできあがってきた。言語や実装方法まで踏み込んで詳細に指示するとかなり良い感じ。あとはSIMDを活用して高速化できる部分をSIMD化しないと。
July 2, 2025 at 2:13 AM
BLASTNに代わる塩基配列検索システムを開発している。Claude Codeのおかげでかなりできあがってきた。言語や実装方法まで踏み込んで詳細に指示するとかなり良い感じ。あとはSIMDを活用して高速化できる部分をSIMD化しないと。
Authors published a paper in Biorxiv, they used BLASTN in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing
www.biorxiv.org
June 27, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used BLASTN in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing