User: jvire1

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jvire110
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Posts by jvire1

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Answer: A: PlantTFDB transcription factor discovery.
... Having slept on it I realized a solution would be to take the transcripts with blastp and blastx hits and analyze them with the PlantTFDB prediction server, which uses a much more robust method to determine homology and has limits on the size of uploaded sequences. ...
written 7 weeks ago by jvire110
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PlantTFDB transcription factor discovery.
... Hi all, I have assembled three transcriptomes of a non-model plant and have been writing up a report. Initially, I blastx and blastp [E-value 1e-5] queried the unigenes and coded for proteins against the entire collection of PlantTFDB protein sequences. Upon analyzing the unigene blastx and blastp ...
rna-seq written 7 weeks ago by jvire110
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Comment: C: Pulling out gene names from a FASTA file with a list of IDs
... Thank you so much! This worked and I was impressed how fast it processed everything. I am still going to see if I can get the solution in python, because I will likely need to be able to do similar tasks and it would be nice to know how to do it myself. Here is the output: NF-YA NF-YA ...
written 10 weeks ago by jvire110
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Comment: C: Pulling out gene names from a FASTA file with a list of IDs
... Thank you for all your help. Here is three FASTA entries in the PlantTFDB FASTA file, with the first one corresponding to the first accession ID in the acc_list.txt: >Zpz_sc04830.1.g00020.1.sm.mk Zoysia pacifica|NF-YA|NF-YA family protein MEAKFFRFLKLVGVGFKARSESQGRELFLKLGYSHEVLFTAPPAVRVFC ...
written 10 weeks ago by jvire110
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Comment: C: Pulling out gene names from a FASTA file with a list of IDs
... Thank you for this awk approach, unfortunately I am needing each line in the accession to be searched one at a time against the FASTA database, retaining duplicate instances. The idea here was to take the accessions and get back the gene name for each. For example an acc.txt file that looked like th ...
written 10 weeks ago by jvire110
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Comment: C: Combining two columns in a tab-delimited file where there is a zero in one
... Thank you, that is much cleaner. ...
written 10 weeks ago by jvire110
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Comment: C: Combining two columns in a tab-delimited file where there is a zero in one
... Thank you so much for this one liner and to all those who helped. Combined these scripts have allowed me to achieve my goal: Bhlh 533 Myb_Related 397 C2H2 355 Nac 352 C3H 337 Erf 297 Myb 265 Wrky 263 B3 249 Bzip 217 Far1 196 G2-Like 167 Gras 157 ...
written 10 weeks ago by jvire110
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Comment: C: Combining two columns in a tab-delimited file where there is a zero in one
... Finally LibreOffice unfroze (wish I could force it to use all 4 cpu)! Here is an example of the columns: PlantTFDB_ALL_TF_pep_BLASTX PlantTFDB_ALL_TF_pep_BLASTP Zpz_sc04830.1.g00020.1.sm.mk^Zpz_sc04830.1.g00020.1.sm.mk^Q:488-228,H:5-93^44.94%ID^E:6e-15^.^. Zpz_sc04830.1.g00020.1.sm.mk^Zpz_ ...
written 10 weeks ago by jvire110
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Comment: C: Combining two columns in a tab-delimited file where there is a zero in one
... Sure, LibreOffice is frozen at the moment the two columns are TAB delimited and the annotations within are delimited with '^'. The identifier I need is the one before the first ^, however my plan was to take the new list of annotations and open in LibreOffice, specifying it as '^' delimited and then ...
written 10 weeks ago by jvire110
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Combining two columns in a tab-delimited file where there is a zero in one
... Hi all, I am currently trying to fill in annotations from a BLASTP of the same database into rows that are 0 in the BLASTX. The columns look like this: BLASTX BLASTP annot1 annot1 annot 2 0 0 annot3 In this example I want "annot3" to be moved under the BLASTX c ...
rna-seq written 10 weeks ago by jvire110 • updated 10 weeks ago by kashifalikhan00740

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