Changelogs » Prost

Prost

0.7.59

*Prost!* (PRocessing Of Short Transcripts) can analyze smallRNA sequencing data generated on any sequencing platform. *Prost!* does not rely on existing annotation to filter sequencing reads but instead starts by aligning all the reads on a user-provided genomic reference, allowing the study of miRNAs in any species. Additionally, any number of samples can be studied together in a single *Prost!* run, allowing an accurate analysis of an entire dataset. After grouping the processed reads by genomic location, *Prost!* then annotates them using a user-defined annotation database (public or personal annotation database). Genomic alignment, grouping, and then annotation enable the study of potentially novel miRNAs, as well as permitting the retention of all the isomiRs that a miRNA may display. Finally *Prost!* contains additional features such as grouping by seed sequence for a more functional approach of the dataset, provides automatic discovery of potential mirror-miRNAs, and analyzes the frequency of various types of post-transcriptional modifications at each genomic location. Each step of the *Prost!* analysis is provided in an Excel output file so that the user have access to all information for deeper analysis of specific cases.

0.7.58

*Prost!* (PRocessing Of Short Transcripts) can analyze smallRNA sequencing data generated on any sequencing platform. *Prost!* does not rely on existing annotation to filter sequencing reads but instead starts by aligning all the reads on a user-provided genomic reference, allowing the study of miRNAs in any species. Additionally, any number of samples can be studied together in a single *Prost!* run, allowing an accurate analysis of an entire dataset. After grouping the processed reads by genomic location, *Prost!* then annotates them using a user-defined annotation database (public or personal annotation database). Genomic alignment, grouping, and then annotation enable the study of potentially novel miRNAs, as well as permitting the retention of all the isomiRs that a miRNA may display. Finally *Prost!* contains additional features such as grouping by seed sequence for a more functional approach of the dataset, provides automatic discovery of potential mirror-miRNAs, and analyzes the frequency of various types of post-transcriptional modifications at each genomic location. Each step of the *Prost!* analysis is provided in an Excel output file so that the user have access to all information for deeper analysis of specific cases.

0.7.56

*Prost!* (PRocessing Of Short Transcripts) can analyze smallRNA sequencing data generated on any sequencing platform. *Prost!* does not rely on existing annotation to filter sequencing reads but instead starts by aligning all the reads on a user-provided genomic reference, allowing the study of miRNAs in any species. Additionally, any number of samples can be studied together in a single *Prost!* run, allowing an accurate analysis of an entire dataset. After grouping the processed reads by genomic location, *Prost!* then annotates them using a user-defined annotation database (public or personal annotation database). Genomic alignment, grouping, and then annotation enable the study of potentially novel miRNAs, as well as permitting the retention of all the isomiRs that a miRNA may display. Finally *Prost!* contains additional features such as grouping by seed sequence for a more functional approach of the dataset, provides automatic discovery of potential mirror-miRNAs, and analyzes the frequency of various types of post-transcriptional modifications at each genomic location. Each step of the *Prost!* analysis is provided in an Excel output file so that the user have access to all information for deeper analysis of specific cases.

0.7.55

*Prost!* (PRocessing Of Short Transcripts) can analyze smallRNA sequencing data generated on any sequencing platform. *Prost!* does not rely on existing annotation to filter sequencing reads but instead starts by aligning all the reads on a user-provided genomic reference, allowing the study of miRNAs in any species. Additionally, any number of samples can be studied together in a single *Prost!* run, allowing an accurate analysis of an entire dataset. After grouping the processed reads by genomic location, *Prost!* then annotates them using a user-defined annotation database (public or personal annotation database). Genomic alignment, grouping, and then annotation enable the study of potentially novel miRNAs, as well as permitting the retention of all the isomiRs that a miRNA may display. Finally *Prost!* contains additional features such as grouping by seed sequence for a more functional approach of the dataset, provides automatic discovery of potential mirror-miRNAs, and analyzes the frequency of various types of post-transcriptional modifications at each genomic location. Each step of the *Prost!* analysis is provided in an Excel output file so that the user have access to all information for deeper analysis of specific cases.

0.7.54

Prost! (PRocessing Of Short Transcripts) can analyze smallRNA sequencing data generated on any sequencing platform. Prost! does not rely on existing annotation to filter sequencing reads but instead starts by aligning all the reads on a user-provided genomic reference, allowing the study of miRNAs in any species. Additionally, any number of samples can be studied together in a single Prost! run, allowing an accurate analysis of an entire dataset. After grouping the processed reads by genomic location, Prost! then annotates them using a user-defined annotation database (public or personal annotation database). Genomic alignment, grouping, and then annotation enable the study of potentially novel miRNAs, as well as permitting the retention of all the isomiRs that a miRNA may display. Finally Prost! contains additional features such as grouping by seed sequence for a more functional approach of the dataset, provides automatic discovery of potential mirror-miRNAs, and analyzes the frequency of various types of post-transcriptional modifications at each genomic location. Each step of the Prost! analysis is provided in an Excel output file so that the user have access to all information for deeper analysis of specific cases.

0.7.53

Prost! (PRocessing Of Small Transcripts) is a python application that quantifies and annotates microRNA (miRNA) expression in metazoans with assembled genomes. Prost! works by counting short transcripts within a user-specifiable length range. These counted transcripts are aligned to a user specifiable genome allowing for post-transcriptional modification (e.g. untemplated additions, editing, alternative cutting) and then "binned" together based on genomic location. Each bin is then annotated with databases of mature miRNAs, hairpins, and other types of RNAs (the databases may be derived from miRBase, Ensembl's BioMart, other databases, or may be custom built by the user).

0.7.52

Prost! (PRocessing Of Small Transcripts) is a python application that quantifies and annotates microRNA (miRNA) expression in metazoans with assembled genomes. Prost! works by counting short transcripts within a user-specifiable length range. These counted transcripts are aligned to a user specifiable genome allowing for post-transcriptional modification (e.g. untemplated additions, editing, alternative cutting) and then "binned" together based on genomic location. Each bin is then annotated with databases of mature miRNAs, hairpins, and other types of RNAs (the databases may be derived from miRBase, Ensembl's BioMart, other databases, or may be custom built by the user).

0.7.51

Prost! (PRocessing Of Small Transcripts) is a python application that quantifies and annotates microRNA (miRNA) expression in metazoans with assembled genomes. Prost! works by counting short transcripts within a user-specifiable length range. These counted transcripts are aligned to a user specifiable genome allowing for post-transcriptional modification (e.g. untemplated additions, editing, alternative cutting) and then "binned" together based on genomic location. Each bin is then annotated with databases of mature miRNAs, hairpins, and other types of RNAs (the databases may be derived from miRBase, Ensembl's BioMart, other databases, or may be custom built by the user).

0.7.50

Prost! (PRocessing Of Small Transcripts) is a python application that quantifies and annotates microRNA (miRNA) expression in metazoans with assembled genomes. Prost! works by counting short transcripts within a user-specifiable length range. These counted transcripts are aligned to a user specifiable genome allowing for post-transcriptional modification (e.g. untemplated additions, editing, alternative cutting) and then "binned" together based on genomic location. Each bin is then annotated with databases of mature miRNAs, hairpins, and other types of RNAs (the databases may be derived from miRBase, Ensembl's BioMart, other databases, or may be custom built by the user).

0.7.49

Prost! (PRocessing Of Small Transcripts) is a python application that quantifies and annotates microRNA (miRNA) expression in metazoans with assembled genomes. Prost! works by counting short transcripts within a user-specifiable length range. These counted transcripts are aligned to a user specifiable genome allowing for post-transcriptional modification (e.g. untemplated additions, editing, alternative cutting) and then "binned" together based on genomic location. Each bin is then annotated with databases of mature miRNAs, hairpins, and other types of RNAs (the databases may be derived from miRBase, Ensembl's BioMart, other databases, or may be custom built by the user).

0.7.48

Prost! (PRocessing Of Small Transcripts) is a python application that quantifies and annotates microRNA (miRNA) expression in metazoans with assembled genomes. Prost! works by counting short transcripts within a user-specifiable length range. These counted transcripts are aligned to a user specifiable genome allowing for post-transcriptional modification (e.g. untemplated additions, editing, alternative cutting) and then "binned" together based on genomic location. Each bin is then annotated with databases of mature miRNAs, hairpins, and other types of RNAs (the databases may be derived from miRBase, Ensembl's BioMart, other databases, or may be custom built by the user).

0.7.47

Prost! (PRocessing Of Small Transcripts) is a python application that quantifies and annotates microRNA (miRNA) expression in metazoans with assembled genomes. Prost! works by counting short transcripts within a user-specifiable length range. These counted transcripts are aligned to a user specifiable genome allowing for post-transcriptional modification (e.g. untemplated additions, editing, alternative cutting) and then "binned" together based on genomic location. Each bin is then annotated with databases of mature miRNAs, hairpins, and other types of RNAs (the databases may be derived from miRBase, Ensembl's BioMart, other databases, or may be custom built by the user).

0.7.46

_Prost!_ (PRocessing Of Small Transcripts) is a python application that quantifies and annotates microRNA (miRNA) expression in metazoans with assembled genomes.  _Prost!_ works by counting short transcripts within a user-specifiable length range.  These counted transcripts are aligned to a user specifiable genome allowing for post-transcriptional modification (e.g. untemplated additions, editing, alternative cutting) and then "binned" together based on genomic location.  Each bin is then annotated with databases of mature miRNAs, hairpins, and other types of RNAs (the databases may be derived from miRBase, Ensembl's BioMart, other databases, or may be custom built by the user).

0.7.45

_Prost!_ (PRocessing Of Small Transcripts) is a python application that quantifies and annotates microRNA (miRNA) expression in metazoans with assembled genomes.  _Prost!_ works by counting short transcripts within a user-specifiable length range.  These counted transcripts are aligned to a user specifiable genome allowing for post-transcriptional modification (e.g. untemplated additions, editing, alternative cutting) and then "binned" together based on genomic location.  Each bin is then annotated with databases of mature miRNAs, hairpins, and other types of RNAs (the databases may be derived from miRBase, Ensembl's BioMart, other databases, or may be custom built by the user).

0.7.42

_Prost!_ (PRocessing Of Small Transcripts) is a python application that quantifies and annotates microRNA (miRNA) expression in metazoans with assembled genomes.  _Prost!_ works by counting short transcripts within a user-specifiable length range.  These counted transcripts are aligned to a user specifiable genome allowing for post-transcriptional modification (e.g. untemplated additions, editing, alternative cutting) and then "binned" together based on genomic location.  Each bin is then annotated with databases of mature miRNAs, hairpins, and other types of RNAs (the databases may be derived from miRBase, Ensembl's BioMart, other databases, or may be custom built by the user).

0.7.35

_Prost!_ (PRocessing Of Small Transcripts) is a python application that quantifies and annotates microRNA (miRNA) expression in metazoans with assembled genomes.  _Prost!_ works by counting short transcripts within a user-specifiable length range.  These counted transcripts are aligned to a user specifiable genome allowing for post-transcriptional modification (e.g. untemplated additions, editing, alternative cutting) and then "binned" together based on genomic location.  Each bin is then annotated with databases of mature miRNAs, hairpins, and other types of RNAs (the databases may be derived from miRBase, Ensembl's BioMart, other databases, or may be custom built by the user).

0.7.34

_Prost!_ (PRocessing Of Small Transcripts) is a python application that quantifies and annotates microRNA (miRNA) expression in chordates and vertebrates with assembled genomes. _Prost!_ works by counting short transcripts within a user-specifiable length range. These counted transcripts are aligned to a user specifiable genome allowing for post-transcriptional modification (e.g. untemplated additions, editing, alternative cutting) and then “binned” together based on genomic location. Each bin is then annotated with miRBase mature sequences and hairpins, as well as other types of RNA obtained from Ensembl’s Biomart.

0.7.31

_Prost!_ (PRocessing Of Small Transcripts) is a python application that quantifies and annotates microRNA (miRNA) expression in chordates and vertebrates with assembled genomes. _Prost!_ works by counting short transcripts within a user-specifiable length range. These counted transcripts are aligned to a user specifiable genome allowing for post-transcriptional modification (e.g. untemplated additions, editing, alternative cutting) and then “binned” together based on genomic location. Each bin is then annotated with miRBase mature sequences and hairpins, as well as other types of RNA obtained from Ensembl’s Biomart.

0.7.29

This is a release of _Prost!_ to be tagged with a DOI by Zenodo, so that _Prost!_ is citable.

0.7.27

This release of _Prost!_ includes a possible fix to reduce memory consumption for certain data sets.  Specifically, by setting the `max_locations_allowed` configuration option (default 40), then for any sequence which hits to the genome more than `max_locations_allowed` times, that sequence's genomic_locations not recorded (they are reported as **MAL** (i.e. maximum allowed locations)).

0.7.9

A small fix to allow _Prost!_ to handle cases where the best alignment to the reference genome overlaps a region with 'N's.

0.7.6

This is the stable release of _Prost!_.

0.7.5

This is the initial release of _Prost!_.